From d3824fc976c4f1ac3b8bcbd4f1e69cc7d98c03e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Fri, 12 Apr 2024 10:50:37 -0400 Subject: [PATCH 01/11] feat: transition to convert_case --- Cargo.toml | 1 + wdl-core/Cargo.toml | 2 +- wdl-core/src/concern/lint.rs | 4 ++-- wdl-core/src/concern/validation.rs | 4 ++-- wdl-grammar/Cargo.toml | 1 + 5 files changed, 7 insertions(+), 5 deletions(-) diff --git a/Cargo.toml b/Cargo.toml index c7acfd3b..8a3adf57 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -17,6 +17,7 @@ version = "0.2.0" [workspace.dependencies] clap = { version = "4.4.7", features = ["derive"] } colored = "2.0.4" +convert_case = "0.6.0" env_logger = "0.10.0" indexmap = { version = "2.1.0", features = ["serde"] } lazy_static = "1.4.0" diff --git a/wdl-core/Cargo.toml b/wdl-core/Cargo.toml index e2a8e987..8df5fb3c 100644 --- a/wdl-core/Cargo.toml +++ b/wdl-core/Cargo.toml @@ -9,8 +9,8 @@ edition.workspace = true [dependencies] clap.workspace = true +convert_case.workspace = true lazy_static.workspace = true nonempty.workspace = true pest.workspace = true serde.workspace = true -to_snake_case = "0.1.1" diff --git a/wdl-core/src/concern/lint.rs b/wdl-core/src/concern/lint.rs index 2f0484da..1ebee0d2 100644 --- a/wdl-core/src/concern/lint.rs +++ b/wdl-core/src/concern/lint.rs @@ -2,8 +2,8 @@ use std::collections::VecDeque; +use convert_case::{Case, Casing}; use nonempty::NonEmpty; -use to_snake_case::ToSnakeCase as _; use crate::concern::Code; use crate::file::location; @@ -68,7 +68,7 @@ impl Linter { pub trait Rule: std::fmt::Debug + Sync { /// The name of the lint rule. fn name(&self) -> String { - format!("{:?}", self).to_snake_case() + format!("{:?}", self).to_case(Case::Snake) } /// Get the code for this lint rule. diff --git a/wdl-core/src/concern/validation.rs b/wdl-core/src/concern/validation.rs index e16fe7bd..b014db4e 100644 --- a/wdl-core/src/concern/validation.rs +++ b/wdl-core/src/concern/validation.rs @@ -2,8 +2,8 @@ use std::collections::VecDeque; +use convert_case::{Case, Casing}; use nonempty::NonEmpty; -use to_snake_case::ToSnakeCase as _; use crate::concern::Code; use crate::file::location; @@ -66,7 +66,7 @@ pub trait Rule: std::fmt::Debug + Sync { /// This is what will show up in style guides, it is required to be snake /// case (even though the rust struct is camel case). fn name(&self) -> String { - format!("{:?}", self).to_snake_case() + format!("{:?}", self).to_case(Case::Snake) } /// Get the code for this validation rule. diff --git a/wdl-grammar/Cargo.toml b/wdl-grammar/Cargo.toml index 23d7e243..d11888b0 100644 --- a/wdl-grammar/Cargo.toml +++ b/wdl-grammar/Cargo.toml @@ -12,6 +12,7 @@ documentation = "https://docs.rs/wdl-grammar" [dependencies] clap = { workspace = true, optional = true } colored = { workspace = true, optional = true } +convert_case.workspace = true env_logger = { workspace = true, optional = true } indexmap = { workspace = true, optional = true } log = { workspace = true, optional = true } From a41d5002a740b98dc2aecf108a0eef80a7cc2dff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Fri, 12 Apr 2024 10:51:54 -0400 Subject: [PATCH 02/11] feat: adding Naming lint gorup --- wdl-core/src/concern/lint/group.rs | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/wdl-core/src/concern/lint/group.rs b/wdl-core/src/concern/lint/group.rs index 88ac3e6b..e1c4dbf9 100644 --- a/wdl-core/src/concern/lint/group.rs +++ b/wdl-core/src/concern/lint/group.rs @@ -9,6 +9,9 @@ pub enum Group { /// Rules associated with having a complete document. Completeness, + /// Rules associated with the names of WDL elements. + Naming, + /// Rules associated with the style of a document. Style, @@ -22,6 +25,7 @@ impl std::fmt::Display for Group { fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { match self { Group::Completeness => write!(f, "Completeness"), + Group::Naming => write!(f, "Naming"), Group::Style => write!(f, "Style"), Group::Pedantic => write!(f, "Pedantic"), } From 8f9633e15808b578e209e3b1f91deae207961a8c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Fri, 12 Apr 2024 12:45:57 -0400 Subject: [PATCH 03/11] feat: adding snake-case rule --- wdl-grammar/src/v1/lint.rs | 4 + wdl-grammar/src/v1/lint/snake_case.rs | 120 ++++++++++++++++++++++++++ wdl-grammar/src/v1/wdl.pest | 3 +- 3 files changed, 126 insertions(+), 1 deletion(-) create mode 100644 wdl-grammar/src/v1/lint/snake_case.rs diff --git a/wdl-grammar/src/v1/lint.rs b/wdl-grammar/src/v1/lint.rs index 1426931b..8e501ff7 100644 --- a/wdl-grammar/src/v1/lint.rs +++ b/wdl-grammar/src/v1/lint.rs @@ -4,10 +4,12 @@ use pest::iterators::Pair; mod mixed_indentation; mod no_curly_commands; +mod snake_case; mod whitespace; pub use mixed_indentation::MixedIndentation; pub use no_curly_commands::NoCurlyCommands; +pub use snake_case::NotSnakeCase; pub use whitespace::Whitespace; /// Gets all WDL v1.x parse tree lint rules. @@ -19,5 +21,7 @@ pub fn rules<'a>() -> Vec NotSnakeCase { + fn not_snake_case(&self, warning: SnakeCaseWarning<'_>) -> lint::Warning + where + Self: Rule<&'a Pair<'a, v1::Rule>>, + { + lint::warning::Builder::default() + .code(self.code()) + .level(lint::Level::Low) + .group(self.group()) + .subject("missing snake case") + .body("Declaration must be formatted using snake case.") + .push_location(warning.location) + .fix(format!( + "Replace {0} by {1}", + warning.declaration, warning.cased_declaration + )) + .try_build() + .unwrap() + } +} + +struct SnakeCaseWarning<'a> { + location: Location, + declaration: &'a str, + cased_declaration: &'a str, +} + +impl Rule<&Pair<'_, v1::Rule>> for NotSnakeCase { + fn code(&self) -> Code { + Code::try_new(code::Kind::Warning, Version::V1, 5).unwrap() + } + + fn group(&self) -> lint::Group { + Group::Naming + } + + fn check(&self, tree: &Pair<'_, v1::Rule>) -> lint::Result { + let mut warnings = VecDeque::new(); + + for node in tree.clone().into_inner().flatten() { + if [ + crate::v1::Rule::task_name, + crate::v1::Rule::workflow_name, + crate::v1::Rule::bound_declaration_name, + crate::v1::Rule::unbound_declaration_name, + ] + .contains(&node.as_rule()) + { + let declaration: &str = node.as_span().as_str(); + let cased_declaration: &str = &node.as_span().as_str().to_case(Case::Snake); + if declaration != cased_declaration { + let warning = SnakeCaseWarning { + location: Location::try_from(node.as_span()) + .map_err(lint::Error::Location)?, + declaration, + cased_declaration, + }; + warnings.push_back(NotSnakeCase.not_snake_case(warning)); + } + } + } + + match warnings.pop_front() { + Some(front) => { + let mut results = NonEmpty::new(front); + results.extend(warnings); + Ok(Some(results)) + } + None => Ok(None), + } + } +} + +#[cfg(test)] +mod tests { + use pest::Parser as _; + use wdl_core::concern::lint::Rule as _; + + use super::*; + use crate::v1::parse::Parser; + use crate::v1::Rule; + + #[test] + fn it_catches_wrong_task_name() -> Result<(), Box> { + let tree = Parser::parse( + Rule::task, + "task thisBad { + command <<< >>> + }", + )? + .next() + .unwrap(); + let warnings = NotSnakeCase.check(&tree)?.unwrap(); + + assert_eq!(warnings.len(), 1); + assert_eq!( + warnings.first().to_string(), + "[v1::W005::Naming/Low] missing snake case (1:6-1:13)" + ); + Ok(()) + } +} diff --git a/wdl-grammar/src/v1/wdl.pest b/wdl-grammar/src/v1/wdl.pest index e21781bc..25312166 100644 --- a/wdl-grammar/src/v1/wdl.pest +++ b/wdl-grammar/src/v1/wdl.pest @@ -469,7 +469,8 @@ task_element = { | metadata } -task = { "task" ~ singular_identifier ~ "{" ~ task_element+ ~ "}" } +task_name = { singular_identifier } +task = { "task" ~ task_name ~ "{" ~ task_element+ ~ "}" } // ========= // // Workflows // From 386fd83af180f36649f2b89b44186ca523b104b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Fri, 12 Apr 2024 12:54:13 -0400 Subject: [PATCH 04/11] feat: renaming lint rule --- wdl-grammar/src/v1.rs | 1 + wdl-grammar/src/v1/lint.rs | 4 ++-- wdl-grammar/src/v1/lint/snake_case.rs | 15 ++++++++------- 3 files changed, 11 insertions(+), 9 deletions(-) diff --git a/wdl-grammar/src/v1.rs b/wdl-grammar/src/v1.rs index db75ccc2..b1b096c8 100644 --- a/wdl-grammar/src/v1.rs +++ b/wdl-grammar/src/v1.rs @@ -21,6 +21,7 @@ //! | `no_curly_commands` | `v1::W002` | Pedantic | [Link](lint::NoCurlyCommands) | //! | `mixed_indentation` | `v1::W004` | Style | [Link](lint::MixedIndentation) | //! | `missing_runtime_block` | `v1::W005` |Completeness | [Link](lint::MissingRuntimeBlock) | +//! | `snake_case` | `v1::W006` | Naming | [Link](lint::SnakeCase) | use pest::iterators::Pair; use pest::Parser as _; diff --git a/wdl-grammar/src/v1/lint.rs b/wdl-grammar/src/v1/lint.rs index 65d93503..b75e70c9 100644 --- a/wdl-grammar/src/v1/lint.rs +++ b/wdl-grammar/src/v1/lint.rs @@ -11,7 +11,7 @@ mod whitespace; pub use missing_runtime_block::MissingRuntimeBlock; pub use mixed_indentation::MixedIndentation; pub use no_curly_commands::NoCurlyCommands; -pub use snake_case::NotSnakeCase; +pub use snake_case::SnakeCase; pub use whitespace::Whitespace; /// Gets all WDL v1.x parse tree lint rules. @@ -26,6 +26,6 @@ pub fn rules<'a>() -> Vec NotSnakeCase { +impl<'a> SnakeCase { fn not_snake_case(&self, warning: SnakeCaseWarning<'_>) -> lint::Warning where Self: Rule<&'a Pair<'a, v1::Rule>>, @@ -43,7 +44,7 @@ struct SnakeCaseWarning<'a> { cased_declaration: &'a str, } -impl Rule<&Pair<'_, v1::Rule>> for NotSnakeCase { +impl Rule<&Pair<'_, v1::Rule>> for SnakeCase { fn code(&self) -> Code { Code::try_new(code::Kind::Warning, Version::V1, 5).unwrap() } @@ -73,7 +74,7 @@ impl Rule<&Pair<'_, v1::Rule>> for NotSnakeCase { declaration, cased_declaration, }; - warnings.push_back(NotSnakeCase.not_snake_case(warning)); + warnings.push_back(SnakeCase.not_snake_case(warning)); } } } @@ -108,12 +109,12 @@ mod tests { )? .next() .unwrap(); - let warnings = NotSnakeCase.check(&tree)?.unwrap(); + let warnings = SnakeCase.check(&tree)?.unwrap(); assert_eq!(warnings.len(), 1); assert_eq!( warnings.first().to_string(), - "[v1::W005::Naming/Low] missing snake case (1:6-1:13)" + "[v1::W006::Naming/Low] missing snake case (1:6-1:13)" ); Ok(()) } From fa37e46fa88d2934259464905ccc4bb964e7a36c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Fri, 12 Apr 2024 13:09:18 -0400 Subject: [PATCH 05/11] doc: adding rule to RULES.md --- RULES.md | 3 ++- wdl-grammar/src/v1/lint/snake_case.rs | 6 +++++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/RULES.md b/RULES.md index 3f6f1b4c..178d255d 100644 --- a/RULES.md +++ b/RULES.md @@ -21,7 +21,8 @@ repository. Note that the information may be out of sync with released packages. | `no_curly_commands` | `v1::W002` | Pedantic | [`wdl-grammar`][wdl-grammar-lints] | | `matching_parameter_meta` | `v1::W003` | Completeness | [`wdl-ast`][wdl-ast-lints] | | `mixed_indentation` | `v1::W004` | Style | [`wdl-grammar`][wdl-grammar-lints] | -| `missing_runtime_block` | `v1::W005` | Completeness | [`wdl-grammar`][wdl-grammar-lints] | +| `missing_runtime_block` | `v1::W005` | Completeness | [`wdl-grammar`][wdl-grammar-lints] | +| `snake_case` | `v1::W006` | Naming | [`wdl-grammar`][wdl-grammar-lints] | [wdl-ast-lints]: https://docs.rs/wdl-ast/latest/wdl_ast/v1/index.html#lint-rules [wdl-ast-validation]: https://docs.rs/wdl-ast/latest/wdl_ast/v1/index.html#validation-rules diff --git a/wdl-grammar/src/v1/lint/snake_case.rs b/wdl-grammar/src/v1/lint/snake_case.rs index 255714a0..7d45db18 100644 --- a/wdl-grammar/src/v1/lint/snake_case.rs +++ b/wdl-grammar/src/v1/lint/snake_case.rs @@ -14,6 +14,10 @@ use wdl_core::Version; use crate::v1; +/// Detects names that should use snake case. +/// +/// Workflows, tasks and variables should be declared +/// using snake case. #[derive(Debug)] pub struct SnakeCase; @@ -46,7 +50,7 @@ struct SnakeCaseWarning<'a> { impl Rule<&Pair<'_, v1::Rule>> for SnakeCase { fn code(&self) -> Code { - Code::try_new(code::Kind::Warning, Version::V1, 5).unwrap() + Code::try_new(code::Kind::Warning, Version::V1, 6).unwrap() } fn group(&self) -> lint::Group { From e9d0b135cd07164729db3b9140d87e40dda5f5ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Fri, 12 Apr 2024 14:38:50 -0400 Subject: [PATCH 06/11] test: adding more test-cases --- wdl-grammar/src/v1/lint/snake_case.rs | 61 ++++++++++++++++++++++++++- 1 file changed, 59 insertions(+), 2 deletions(-) diff --git a/wdl-grammar/src/v1/lint/snake_case.rs b/wdl-grammar/src/v1/lint/snake_case.rs index 7d45db18..ad03dbcd 100644 --- a/wdl-grammar/src/v1/lint/snake_case.rs +++ b/wdl-grammar/src/v1/lint/snake_case.rs @@ -107,9 +107,9 @@ mod tests { fn it_catches_wrong_task_name() -> Result<(), Box> { let tree = Parser::parse( Rule::task, - "task thisBad { + r#"task thisBad { command <<< >>> - }", + }"#, )? .next() .unwrap(); @@ -122,4 +122,61 @@ mod tests { ); Ok(()) } + + #[test] + fn it_catches_wrong_workflow_name() -> Result<(), Box> { + let tree = Parser::parse( + Rule::workflow, + r#"workflow thisBadWorkflow { + Int variable = 1 + }"#, + )? + .next() + .unwrap(); + let warnings = SnakeCase.check(&tree)?.unwrap(); + + assert_eq!(warnings.len(), 1); + assert_eq!( + warnings.first().to_string(), + "[v1::W006::Naming/Low] missing snake case (1:10-1:25)" + ); + Ok(()) + } + + #[test] + fn it_catches_wrong_variable_name() -> Result<(), Box> { + let tree = Parser::parse( + Rule::workflow, + r#"workflow this_workflow { + Int wrongVariable = 1 + }"#, + )? + .next() + .unwrap(); + let warnings = SnakeCase.check(&tree)?.unwrap(); + + assert_eq!(warnings.len(), 1); + assert_eq!( + warnings.first().to_string(), + "[v1::W006::Naming/Low] missing snake case (2:21-2:34)" + ); + Ok(()) + } + + #[test] + fn it_does_not_catch_struct_name() -> Result<(), Box> { + let tree = Parser::parse( + Rule::document, + r#"version 1.0 + struct myStruct { + String my_string + Int my_int + }"#, + )? + .next() + .unwrap(); + let warnings = SnakeCase.check(&tree)?; + assert!(warnings.is_none()); + Ok(()) + } } From 1df955f627ade1eb7130dd9e5911535df05101c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Fri, 12 Apr 2024 15:46:30 -0400 Subject: [PATCH 07/11] docs: updating documentation --- wdl-ast/src/v1/document/task.rs | 6 +++--- wdl-core/src/concern/lint.rs | 3 ++- wdl-core/src/concern/validation.rs | 3 ++- wdl-grammar/src/v1/lint/snake_case.rs | 27 ++++++++++++++++++--------- 4 files changed, 25 insertions(+), 14 deletions(-) diff --git a/wdl-ast/src/v1/document/task.rs b/wdl-ast/src/v1/document/task.rs index 65720adc..a35a8ea7 100644 --- a/wdl-ast/src/v1/document/task.rs +++ b/wdl-ast/src/v1/document/task.rs @@ -451,10 +451,10 @@ impl TryFrom> for Task { for node in node.into_inner() { match node.as_rule() { - Rule::singular_identifier => { - let identifier = Identifier::try_from(node.as_str().to_owned()) + Rule::task_name => { + let name = Identifier::try_from(node.as_str().to_owned()) .map_err(Error::Identifier)?; - builder = builder.name(identifier).map_err(Error::Builder)?; + builder = builder.name(name).map_err(Error::Builder)?; } Rule::task_element => { let node = unwrap_one!(node, task_element); diff --git a/wdl-core/src/concern/lint.rs b/wdl-core/src/concern/lint.rs index 1ebee0d2..ff527272 100644 --- a/wdl-core/src/concern/lint.rs +++ b/wdl-core/src/concern/lint.rs @@ -2,7 +2,8 @@ use std::collections::VecDeque; -use convert_case::{Case, Casing}; +use convert_case::Case; +use convert_case::Casing; use nonempty::NonEmpty; use crate::concern::Code; diff --git a/wdl-core/src/concern/validation.rs b/wdl-core/src/concern/validation.rs index b014db4e..6769e075 100644 --- a/wdl-core/src/concern/validation.rs +++ b/wdl-core/src/concern/validation.rs @@ -2,7 +2,8 @@ use std::collections::VecDeque; -use convert_case::{Case, Casing}; +use convert_case::Case; +use convert_case::Casing; use nonempty::NonEmpty; use crate::concern::Code; diff --git a/wdl-grammar/src/v1/lint/snake_case.rs b/wdl-grammar/src/v1/lint/snake_case.rs index ad03dbcd..35ed4476 100644 --- a/wdl-grammar/src/v1/lint/snake_case.rs +++ b/wdl-grammar/src/v1/lint/snake_case.rs @@ -1,3 +1,5 @@ +//! Workflows, tasks and variables should be in lowered snake case. + use std::collections::VecDeque; use convert_case::Case; @@ -22,6 +24,7 @@ use crate::v1; pub struct SnakeCase; impl<'a> SnakeCase { + /// Creates a warning for identifiers that are not proper snake case. fn not_snake_case(&self, warning: SnakeCaseWarning<'_>) -> lint::Warning where Self: Rule<&'a Pair<'a, v1::Rule>>, @@ -31,21 +34,27 @@ impl<'a> SnakeCase { .level(lint::Level::Low) .group(self.group()) .subject("missing snake case") - .body("Declaration must be formatted using snake case.") + .body("Identifier must be formatted using snake case.") .push_location(warning.location) .fix(format!( "Replace {0} by {1}", - warning.declaration, warning.cased_declaration + warning.identifier, warning.cased_identifier )) .try_build() .unwrap() } } +/// Arguments for the `not_snake_case` function. struct SnakeCaseWarning<'a> { + /// Location of the warning. location: Location, - declaration: &'a str, - cased_declaration: &'a str, + + /// Original identifier + identifier: &'a str, + + /// Properly cased identifier + cased_identifier: &'a str, } impl Rule<&Pair<'_, v1::Rule>> for SnakeCase { @@ -69,14 +78,14 @@ impl Rule<&Pair<'_, v1::Rule>> for SnakeCase { ] .contains(&node.as_rule()) { - let declaration: &str = node.as_span().as_str(); - let cased_declaration: &str = &node.as_span().as_str().to_case(Case::Snake); - if declaration != cased_declaration { + let identifier: &str = node.as_span().as_str(); + let cased_identifier: &str = &node.as_span().as_str().to_case(Case::Snake); + if identifier != cased_identifier { let warning = SnakeCaseWarning { location: Location::try_from(node.as_span()) .map_err(lint::Error::Location)?, - declaration, - cased_declaration, + identifier, + cased_identifier, }; warnings.push_back(SnakeCase.not_snake_case(warning)); } From 5d5c21f448c2e401c4d9641a07b16b2203fa41cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Fri, 12 Apr 2024 17:06:14 -0400 Subject: [PATCH 08/11] chore: updating wdl-grammar changelog --- wdl-grammar/CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/wdl-grammar/CHANGELOG.md b/wdl-grammar/CHANGELOG.md index 9e3e67cb..c1b4d10f 100644 --- a/wdl-grammar/CHANGELOG.md +++ b/wdl-grammar/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 * Adds the `missing_runtime_block` rule for tasks (#10, contributed by @markjschreiber). +* Adds the `snake_case` rule (#11, contributed by @simojoe). ## 0.2.0 - 12-17-2023 From aa0e515a96b03378307d60cca6c970c5d4a26d64 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Fri, 12 Apr 2024 17:08:40 -0400 Subject: [PATCH 09/11] chore: update PR number in changelog --- wdl-grammar/CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-grammar/CHANGELOG.md b/wdl-grammar/CHANGELOG.md index c1b4d10f..899a132a 100644 --- a/wdl-grammar/CHANGELOG.md +++ b/wdl-grammar/CHANGELOG.md @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 * Adds the `missing_runtime_block` rule for tasks (#10, contributed by @markjschreiber). -* Adds the `snake_case` rule (#11, contributed by @simojoe). +* Adds the `snake_case` rule (#13, contributed by @simojoe). ## 0.2.0 - 12-17-2023 From 466fcfbdd563556a35e76cc44ceddeac667c451e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Sun, 28 Apr 2024 16:25:59 -0400 Subject: [PATCH 10/11] feat: adding test and doc for snake_case lint warning --- wdl-grammar/CHANGELOG.md | 3 +- wdl-grammar/src/v1.rs | 2 +- wdl-grammar/src/v1/lint/snake_case.rs | 102 ++++++++++++++++++++------ 3 files changed, 83 insertions(+), 24 deletions(-) diff --git a/wdl-grammar/CHANGELOG.md b/wdl-grammar/CHANGELOG.md index 899a132a..49b9d58d 100644 --- a/wdl-grammar/CHANGELOG.md +++ b/wdl-grammar/CHANGELOG.md @@ -11,7 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 * Adds the `missing_runtime_block` rule for tasks (#10, contributed by @markjschreiber). -* Adds the `snake_case` rule (#13, contributed by @simojoe). +* Adds the `snake_case` rule that ensures all tasks, workflows, and variables + are snakecase (#13, contributed by @simojoe). ## 0.2.0 - 12-17-2023 diff --git a/wdl-grammar/src/v1.rs b/wdl-grammar/src/v1.rs index b1b096c8..9dcbd348 100644 --- a/wdl-grammar/src/v1.rs +++ b/wdl-grammar/src/v1.rs @@ -21,7 +21,7 @@ //! | `no_curly_commands` | `v1::W002` | Pedantic | [Link](lint::NoCurlyCommands) | //! | `mixed_indentation` | `v1::W004` | Style | [Link](lint::MixedIndentation) | //! | `missing_runtime_block` | `v1::W005` |Completeness | [Link](lint::MissingRuntimeBlock) | -//! | `snake_case` | `v1::W006` | Naming | [Link](lint::SnakeCase) | +//! | `snake_case` | `v1::W006` | Naming | [Link](lint::SnakeCase) | use pest::iterators::Pair; use pest::Parser as _; diff --git a/wdl-grammar/src/v1/lint/snake_case.rs b/wdl-grammar/src/v1/lint/snake_case.rs index 35ed4476..3051c8bf 100644 --- a/wdl-grammar/src/v1/lint/snake_case.rs +++ b/wdl-grammar/src/v1/lint/snake_case.rs @@ -1,4 +1,4 @@ -//! Workflows, tasks and variables should be in lowered snake case. +//! Workflows, tasks, and variables should be in snake case. use std::collections::VecDeque; @@ -18,8 +18,7 @@ use crate::v1; /// Detects names that should use snake case. /// -/// Workflows, tasks and variables should be declared -/// using snake case. +/// Workflows, tasks and variables should be declared using snake case. #[derive(Debug)] pub struct SnakeCase; @@ -33,12 +32,12 @@ impl<'a> SnakeCase { .code(self.code()) .level(lint::Level::Low) .group(self.group()) - .subject("missing snake case") + .subject("identifier must be snake case") .body("Identifier must be formatted using snake case.") .push_location(warning.location) .fix(format!( "Replace {0} by {1}", - warning.identifier, warning.cased_identifier + warning.identifier, warning.properly_cased_identifier )) .try_build() .unwrap() @@ -54,7 +53,7 @@ struct SnakeCaseWarning<'a> { identifier: &'a str, /// Properly cased identifier - cased_identifier: &'a str, + properly_cased_identifier: &'a str, } impl Rule<&Pair<'_, v1::Rule>> for SnakeCase { @@ -79,15 +78,14 @@ impl Rule<&Pair<'_, v1::Rule>> for SnakeCase { .contains(&node.as_rule()) { let identifier: &str = node.as_span().as_str(); - let cased_identifier: &str = &node.as_span().as_str().to_case(Case::Snake); - if identifier != cased_identifier { - let warning = SnakeCaseWarning { - location: Location::try_from(node.as_span()) - .map_err(lint::Error::Location)?, + let properly_cased_identifier: &str = &node.as_span().as_str().to_case(Case::Snake); + if identifier != properly_cased_identifier { + warnings.push_back(SnakeCase.not_snake_case(SnakeCaseWarning { + location: + Location::try_from(node.as_span()).map_err(lint::Error::Location)?, identifier, - cased_identifier, - }; - warnings.push_back(SnakeCase.not_snake_case(warning)); + properly_cased_identifier, + })); } } } @@ -116,7 +114,7 @@ mod tests { fn it_catches_wrong_task_name() -> Result<(), Box> { let tree = Parser::parse( Rule::task, - r#"task thisBad { + r#"task wrongName { command <<< >>> }"#, )? @@ -127,16 +125,31 @@ mod tests { assert_eq!(warnings.len(), 1); assert_eq!( warnings.first().to_string(), - "[v1::W006::Naming/Low] missing snake case (1:6-1:13)" + "[v1::W006::Naming/Low] identifier must be snake case (1:6-1:15)" ); Ok(()) } + #[test] + fn it_ignores_a_properly_cased_task_name() -> Result<(), Box> { + let tree = Parser::parse( + Rule::task, + r#"task good_name { + command <<< >>> + }"#, + )? + .next() + .unwrap(); + let warnings = SnakeCase.check(&tree)?; + assert!(warnings.is_none()); + Ok(()) + } + #[test] fn it_catches_wrong_workflow_name() -> Result<(), Box> { let tree = Parser::parse( Rule::workflow, - r#"workflow thisBadWorkflow { + r#"workflow wrongWorkflow { Int variable = 1 }"#, )? @@ -147,31 +160,76 @@ mod tests { assert_eq!(warnings.len(), 1); assert_eq!( warnings.first().to_string(), - "[v1::W006::Naming/Low] missing snake case (1:10-1:25)" + "[v1::W006::Naming/Low] identifier must be snake case (1:10-1:23)" ); Ok(()) } #[test] - fn it_catches_wrong_variable_name() -> Result<(), Box> { + fn it_ignores_a_properly_cased_workflow_name() -> Result<(), Box> { let tree = Parser::parse( Rule::workflow, - r#"workflow this_workflow { - Int wrongVariable = 1 + r#"workflow good_workflow { + Int variable = 1 }"#, )? .next() .unwrap(); + let warnings = SnakeCase.check(&tree)?; + assert!(warnings.is_none()); + Ok(()) + } + + #[test] + fn it_catches_wrong_bound_declaration() -> Result<(), Box> { + let tree = Parser::parse(Rule::bound_declaration, r#"Int wrongVariable = 1"#)? + .next() + .unwrap(); + let warnings = SnakeCase.check(&tree)?.unwrap(); + + assert_eq!(warnings.len(), 1); + assert_eq!( + warnings.first().to_string(), + "[v1::W006::Naming/Low] identifier must be snake case (1:5-1:18)" + ); + Ok(()) + } + + #[test] + fn it_ignores_a_properly_cased_bound_declaration() -> Result<(), Box> { + let tree = Parser::parse(Rule::bound_declaration, r#"Int good_bound = 1"#)? + .next() + .unwrap(); + let warnings = SnakeCase.check(&tree)?; + assert!(warnings.is_none()); + Ok(()) + } + + #[test] + fn it_catches_wrong_unbound_declaration() -> Result<(), Box> { + let tree = Parser::parse(Rule::unbound_declaration, r#"Int wrongVariable"#)? + .next() + .unwrap(); let warnings = SnakeCase.check(&tree)?.unwrap(); assert_eq!(warnings.len(), 1); assert_eq!( warnings.first().to_string(), - "[v1::W006::Naming/Low] missing snake case (2:21-2:34)" + "[v1::W006::Naming/Low] identifier must be snake case (1:5-1:18)" ); Ok(()) } + #[test] + fn it_ignores_a_properly_cased_unbound_declaration() -> Result<(), Box> { + let tree = Parser::parse(Rule::unbound_declaration, r#"Int good_unbound"#)? + .next() + .unwrap(); + let warnings = SnakeCase.check(&tree)?; + assert!(warnings.is_none()); + Ok(()) + } + #[test] fn it_does_not_catch_struct_name() -> Result<(), Box> { let tree = Parser::parse( From 204a56c4e30b3883ba63609fd3734e26ada89160 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=ABl=20Simoneau?= Date: Wed, 1 May 2024 15:33:11 -0400 Subject: [PATCH 11/11] feat: updating Gauntlet.toml for snake_case --- Gauntlet.toml | 51107 ++++++++++++++++++++++++++++++++++++------------ 1 file changed, 38281 insertions(+), 12826 deletions(-) diff --git a/Gauntlet.toml b/Gauntlet.toml index 6fa5d340..fb790a36 100644 --- a/Gauntlet.toml +++ b/Gauntlet.toml @@ -300,6 +300,11 @@ kind = "LintWarning" document = "PacificBiosciences/HiFi-human-WGS-WDL:workflows/sample_analysis/sample_analysis.wdl" message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (335:3-335:11)" +[[concerns]] +kind = "LintWarning" +document = "PacificBiosciences/HiFi-human-WGS-WDL:workflows/sample_analysis/sample_analysis.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (252:6-252:17)" + [[concerns]] kind = "LintWarning" document = "PacificBiosciences/HiFi-human-WGS-WDL:workflows/tertiary_analysis/tertiary_analysis.wdl" @@ -472,32068 +477,57518 @@ message = "[v1::W002::Style/Medium] curly command found (46:5-57:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bam2fastx.wdl" -message = "[v1::W002::Style/Medium] curly command found (106:5-130:6)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:10)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bam2fastx.wdl" -message = "[v1::W002::Style/Medium] curly command found (38:5-62:6)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:16-26:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bam2fastx.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: fastaFile (87:9-87:18)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:14-28:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bam2fastx.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: fastqFile (155:9-155:18)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:15-30:30)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bcftools.wdl" -message = "[v1::W001::Style/Low] trailing space (147:15)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:15-33:35)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bcftools.wdl" -message = "[v1::W002::Style/Medium] curly command found (146:5-158:6)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:24-34:35)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bcftools.wdl" -message = "[v1::W002::Style/Medium] curly command found (196:5-206:6)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:24-35:34)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bcftools.wdl" -message = "[v1::W002::Style/Medium] curly command found (269:5-294:6)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:13-38:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bcftools.wdl" -message = "[v1::W002::Style/Medium] curly command found (361:5-374:6)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (39:16-39:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bcftools.wdl" -message = "[v1::W002::Style/Medium] curly command found (57:5-84:6)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (60:14-60:21)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bedtools.wdl" -message = "[v1::W002::Style/Medium] curly command found (128:5-131:6)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (61:14-61:21)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bedtools.wdl" -message = "[v1::W002::Style/Medium] curly command found (168:5-171:6)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (62:14-62:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bedtools.wdl" -message = "[v1::W002::Style/Medium] curly command found (215:5-229:6)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (63:14-63:19)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bedtools.wdl" -message = "[v1::W002::Style/Medium] curly command found (277:5-286:6)" +document = "biowdl/tasks:CPAT.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (64:14-64:21)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bedtools.wdl" -message = "[v1::W002::Style/Medium] curly command found (36:5-43:6)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W002::Style/Medium] curly command found (106:5-130:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bedtools.wdl" -message = "[v1::W002::Style/Medium] curly command found (83:5-91:6)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W002::Style/Medium] curly command found (38:5-62:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:biowdl.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: json (73:9-73:13)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: fastaFile (87:9-87:18)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bowtie.wdl" -message = "[v1::W002::Style/Medium] curly command found (49:5-71:6)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: fastqFile (155:9-155:18)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bwa-mem2.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (36:1-36:8)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (102:13-102:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bwa-mem2.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (56:1-56:4)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (103:16-103:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bwa-mem2.wdl" -message = "[v1::W002::Style/Medium] curly command found (59:5-76:6)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (133:14-133:23)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bwa-mem2.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputBam (110:9-110:18)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:15)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bwa-mem2.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputHla (111:9-111:18)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:22-26:30)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bwa.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (52:1-52:4)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bwa.wdl" -message = "[v1::W002::Style/Medium] curly command found (126:5-130:6)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:13-28:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bwa.wdl" -message = "[v1::W002::Style/Medium] curly command found (55:5-73:6)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:17-29:31)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bwa.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: index (159:9-159:14)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:17-31:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bwa.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputBam (108:9-108:18)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:13-34:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:bwa.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputHla (109:9-109:18)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case 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parameter meta within task: ccsJsonReport (121:9-121:22)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (95:16-95:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:ccs.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ccsReport (120:9-120:18)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (96:13-96:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:ccs.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ccsStderr (122:9-122:18)" +document = "biowdl/tasks:bam2fastx.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (97:17-97:31)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:ccs.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: zmwMetrics (123:9-123:19)" +document = "biowdl/tasks:bam2fastx.wdl" 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"[v1::W002::Style/Medium] curly command found (38:5-47:6)" +document = "biowdl/tasks:bcftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (135:14-135:22)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:chunked-scatter.wdl" -message = "[v1::W002::Style/Medium] curly command found (94:5-101:6)" +document = "biowdl/tasks:bcftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (138:17-138:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:chunked-scatter.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: scatters (126:9-126:17)" +document = "biowdl/tasks:bcftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (139:16-139:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:chunked-scatter.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: scatters (73:9-73:17)" +document = "biowdl/tasks:bcftools.wdl" 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"[v1::W003::Completeness/Medium] extraneous parameter meta within task: predictions (138:9-138:20)" +document = "biowdl/tasks:bcftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (183:6-183:10)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:collect-columns.wdl" -message = "[v1::W002::Style/Medium] curly command found (43:5-58:6)" +document = "biowdl/tasks:bcftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (185:14-185:23)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:collect-columns.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputTable (88:9-88:20)" +document = "biowdl/tasks:bcftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (186:16-186:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:common.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (27:1-27:8)" +document = "biowdl/tasks:bcftools.wdl" 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"LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W002::Style/Medium] curly command found (487:5-493:6)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (116:10-116:19)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W002::Style/Medium] curly command found (535:5-555:6)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (117:17-117:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W002::Style/Medium] curly command found (613:5-630:6)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:9)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W002::Style/Medium] curly command found (699:5-712:6)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:19)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W002::Style/Medium] curly command found (787:5-826:6)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:15-26:20)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W002::Style/Medium] curly command found (909:5-920:6)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:18-27:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W002::Style/Medium] curly command found (988:5-1009:6)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:16-28:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: 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"[v1::W006::Naming/Low] identifier must be snake case (32:13-32:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputPath (1220:9-1220:44)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:14-35:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: panelOnly (1219:9-1219:34)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:14-38:22)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: purpleGermlineVariantVcfIndex (758:9-758:43)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (39:13-39:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: purpleSomaticVariantVcfIndex (764:9-764:42)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:16-41:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:hmftools.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: threads (1234:9-1234:25)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (47:9-47:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:htseq.wdl" -message = "[v1::W002::Style/Medium] curly command found (41:5-54:6)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (48:9-48:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:htseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: counts (83:9-83:15)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (55:9-55:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:isoseq3.wdl" -message = "[v1::W002::Style/Medium] curly command found (40:5-52:6)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (79:14-79:23)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:isoseq3.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: refineBam (86:9-86:18)" +document = "biowdl/tasks:bwa-mem2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (80:15-80:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:isoseq3.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: refineBamIndex (87:9-87:23)" +document = "biowdl/tasks:bwa.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (52:1-52:4)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:isoseq3.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: refineConsensusReadset (88:9-88:31)" +document = "biowdl/tasks:bwa.wdl" +message = "[v1::W002::Style/Medium] curly command found (126:5-130:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:isoseq3.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: refineFilterSummary (89:9-89:28)" +document = "biowdl/tasks:bwa.wdl" +message = "[v1::W002::Style/Medium] curly command found (55:5-73:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:isoseq3.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: refineReport (90:9-90:21)" +document = "biowdl/tasks:bwa.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: index (159:9-159:14)" [[concerns]] kind = "LintWarning" -document 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parameter meta within task: limaBamIndex (149:9-149:21)" +document = "biowdl/tasks:bwa.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (115:17-115:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:lima.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: limaCounts (153:9-153:19)" +document = "biowdl/tasks:bwa.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (118:6-118:11)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:lima.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: limaJson (152:9-152:17)" +document = "biowdl/tasks:bwa.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (121:16-121:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:lima.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: limaReport (154:9-154:19)" +document = "biowdl/tasks:bwa.wdl" +message = 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[[concerns]] kind = "LintWarning" -document = "biowdl/tasks:minimap2.wdl" -message = "[v1::W002::Style/Medium] curly command found (39:5-50:6)" +document = "biowdl/tasks:bwa.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (51:9-51:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:minimap2.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: alignmentFile (162:9-162:22)" +document = "biowdl/tasks:bwa.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (76:14-76:23)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:minimap2.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: indexFile (77:9-77:18)" +document = "biowdl/tasks:bwa.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (77:15-77:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:multiqc.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace 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"biowdl/tasks:multiqc.wdl" -message = "[v1::W001::Style/Low] trailing space (77:78)" +document = "biowdl/tasks:ccs.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ccsReport (120:9-120:18)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:multiqc.wdl" -message = "[v1::W001::Style/Low] trailing space (84:33)" +document = "biowdl/tasks:ccs.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ccsStderr (122:9-122:18)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:multiqc.wdl" -message = "[v1::W002::Style/Medium] curly command found (81:5-130:6)" +document = "biowdl/tasks:ccs.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: zmwMetrics (123:9-123:19)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:nanopack.wdl" -message = "[v1::W002::Style/Medium] curly command found (138:5-146:6)" +document = "biowdl/tasks:ccs.wdl" +message = 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must be snake case (23:6-23:20)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W002::Style/Medium] curly command found (56:5-80:6)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:22-25:33)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: consensusIndels (245:9-245:24)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:16-26:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: consensusIndels (430:9-430:24)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:17-28:33)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: consensusSNV (246:9-246:21)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:14-30:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: consensusSNV (431:9-431:21)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:14-31:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleIndels (133:9-133:23)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:24-33:35)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleIndels (247:9-247:23)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:24-34:44)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleIndels (341:9-341:23)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:15-35:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleIndels (432:9-432:23)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:17-36:33)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleIndelsClassifier (249:9-249:33)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:13-38:21)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleIndelsClassifier (434:9-434:33)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (39:13-39:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleSNV (134:9-134:20)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (40:16-40:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleSNV (248:9-248:20)" +document = "biowdl/tasks:collect-columns.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (61:14-61:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleSNV (342:9-342:20)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (27:1-27:8)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleSNV (433:9-433:20)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W002::Style/Medium] curly command found (111:5-115:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleSNVClassifier (250:9-250:30)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W002::Style/Medium] curly command found (138:5-140:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleSNVClassifier (435:9-435:30)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W002::Style/Medium] curly command found (197:5-200:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: indels (131:9-131:15)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W002::Style/Medium] curly command found (221:5-224:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: indels (339:9-339:15)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W002::Style/Medium] curly command found (283:5-294:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputVcf (477:9-477:18)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W002::Style/Medium] curly command found (31:5-34:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: snvs (132:9-132:13)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W002::Style/Medium] curly command found (58:5-63:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:somaticseq.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: snvs (340:9-340:13)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W002::Style/Medium] curly command found (85:5-89:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W002::Style/Medium] curly command found (57:5-87:6)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (100:6-100:10)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: careful (44:9-44:32)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (102:14-102:23)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: covCutoff (50:9-50:25)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (103:16-103:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dataset (47:9-47:22)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (108:16-108:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disableGzipOutput (45:9-45:42)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (118:14-118:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disableRepeatResolution (46:9-46:48)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (127:6-127:16)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: interlacedReads (30:9-30:30)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (132:16-132:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ionTorrent (41:9-41:35)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (133:16-133:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: k (49:9-49:18)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (151:6-151:30)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memoryGb (54:9-54:26)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (153:23-153:32)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metagenomic (38:9-38:36)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (157:16-157:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nanoporeReads (33:9-33:28)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (189:6-189:12)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: onlyAssembler (43:9-43:38)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (194:16-194:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: onlyErrorCorrection (42:9-42:44)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (203:16-203:22)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputDir (27:9-27:25)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (213:6-213:20)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pacbioReads (32:9-32:26)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (215:23-215:34)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: phredOffset (51:9-51:25)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (218:16-218:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: plasmid (40:9-40:32)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (227:16-227:22)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preCommand (29:9-29:27)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (236:6-236:16)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read1 (25:9-25:19)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (239:16-239:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read2 (26:9-26:20)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rna (39:9-39:28)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (242:13-242:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sangerReads (31:9-31:26)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (243:16-243:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: singleCell (37:9-37:35)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (272:6-272:16)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: threads (53:9-53:24)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (275:16-275:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tmpDir (48:9-48:21)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (278:13-278:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: trustedContigs (35:9-35:29)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (280:16-280:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tslrContigs (34:9-34:26)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (328:13-328:19)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:spades.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: untrustedContigs (36:9-36:31)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (334:13-334:19)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W001::Style/Low] trailing space (137:87)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (338:10-338:12)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W002::Style/Medium] curly command found (146:5-166:6)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (339:13-339:19)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W002::Style/Medium] curly command found (217:5-219:6)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (340:11-340:13)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W002::Style/Medium] curly command found (37:5-47:6)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (341:13-341:19)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: bamFile (204:9-204:16)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (345:12-345:21)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: chrLength (91:9-91:18)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (346:20-346:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: chrName (93:9-93:16)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (347:12-347:23)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: chrNameLength (92:9-92:22)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (348:20-348:31)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: chrStart (94:9-94:17)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (352:24-352:36)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: exonGeTrInfo (99:9-99:21)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:23-37:31)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: exonInfo (100:9-100:17)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (46:6-46:18)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: geneInfo (101:9-101:17)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (49:16-49:19)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: genome (95:9-95:15)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (55:16-55:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: genomeParameters (96:9-96:25)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (71:6-71:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: logFinalOut (205:9-205:20)" +document = "biowdl/tasks:common.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (73:21-73:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: sa (97:9-97:11)" 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(92:14-92:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: sjdbListOut (104:9-104:20)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W002::Style/Medium] curly command found (98:5-157:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: starIndex (106:9-106:18)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: cutRead1 (243:9-243:17)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: transcriptInfo (105:9-105:23)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: cutRead2 (245:9-245:17)" [[concerns]] kind = "LintWarning" 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"biowdl/tasks:star.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample (211:9-211:22)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: tooLongOutput (246:9-246:22)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:star.wdl" -message = "[v1::W005::Completeness/Medium] missing runtime block within a task (209:1-224:2)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: tooLongPairedOutput (249:9-249:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:strelka.wdl" -message = "[v1::W002::Style/Medium] curly command found (117:5-131:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: tooShortOutput (247:9-247:23)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:strelka.wdl" -message = "[v1::W002::Style/Medium] curly command found (44:5-57:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: tooShortPairedOutput (250:9-250:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:strelka.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: indelsIndex (168:9-168:20)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: untrimmedOutput (248:9-248:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:strelka.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: indelsVcf (167:9-167:18)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: untrimmedPairedOutput (251:9-251:30)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:strelka.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: variants (169:9-169:17)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: wildcardFile (254:9-254:21)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:strelka.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: variants (88:9-88:17)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (160:14-160:22)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:strelka.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: variantsIndex (170:9-170:22)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (162:15-162:23)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:strelka.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: variantsIndex (89:9-89:22)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (163:15-163:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:strelka.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: doNotDefineThis (114:9-114:30)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (164:15-164:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:stringtie.wdl" -message = "[v1::W002::Style/Medium] curly command found (110:5-124:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (165:15-165:30)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:stringtie.wdl" -message = "[v1::W002::Style/Medium] curly command found (42:5-55:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case 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"[v1::W006::Naming/Low] identifier must be snake case (25:14-25:19)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:talon.wdl" -message = "[v1::W002::Style/Medium] curly command found (258:5-266:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:15-26:20)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:talon.wdl" -message = "[v1::W002::Style/Medium] curly command found (310:5-322:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:talon.wdl" -message = "[v1::W002::Style/Medium] curly command found (368:5-379:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:17-28:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:talon.wdl" -message = "[v1::W002::Style/Medium] curly command found (38:5-48:6)" 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"[v1::W003::Completeness/Medium] extraneous parameter meta within task: abundanceFile (73:9-73:22)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:13-41:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:talon.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: databaseFile (349:9-349:21)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (44:17-44:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:talon.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: gtfFile (131:9-131:16)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (45:16-45:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:talon.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: labeledSam 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"[v1::W006::Naming/Low] identifier must be snake case (51:18-51:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:talon.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: spliceJunctions (290:9-290:24)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (52:18-52:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:talon.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: summaryFile (493:9-493:20)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (54:17-54:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:talon.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: talonAnnotation (568:9-568:24)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (55:17-55:30)" [[concerns]] kind 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"[v1::W003::Completeness/Medium] extraneous parameter meta within task: updatedDatabase (566:9-566:24)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (60:17-60:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:transcriptclean.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (193:1-193:8)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (63:14-63:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:transcriptclean.wdl" -message = "[v1::W002::Style/Medium] curly command found (136:5-156:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (64:14-64:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:transcriptclean.wdl" -message = "[v1::W002::Style/Medium] curly command found (35:5-43:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (65:14-65:18)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:transcriptclean.wdl" -message = "[v1::W002::Style/Medium] curly command found (80:5-86:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (66:18-66:32)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:transcriptclean.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: fastaFile (195:9-195:18)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (67:18-67:34)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:transcriptclean.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: logFile (196:9-196:16)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (68:17-68:29)" [[concerns]] kind = "LintWarning" 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"[v1::W003::Completeness/Medium] extraneous parameter meta within task: statsFile (107:9-107:18)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (72:17-72:34)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:umi-tools.wdl" -message = "[v1::W002::Style/Medium] curly command found (38:5-47:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (73:17-73:36)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:umi-tools.wdl" -message = "[v1::W002::Style/Medium] curly command found (97:5-108:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (74:17-74:41)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:umi.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (38:1-38:4)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (75:17-75:40)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:umi.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (40:1-40:4)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (76:17-76:42)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:umi.wdl" -message = "[v1::W001::Style/Low] trailing space (26:79)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (78:18-78:30)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:umi.wdl" -message = "[v1::W001::Style/Low] trailing space (43:21)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (79:18-79:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W002::Style/Medium] curly command found (72:5-117:6)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (82:18-82:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bcftoolsPath (61:9-61:27)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (83:18-83:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2Path (55:9-55:26)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (88:13-88:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2buildPath (56:9-56:31)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (89:16-89:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination (64:9-64:28)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (92:12-92:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: depthFilter (44:9-44:27)" +document = "biowdl/tasks:cutadapt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (93:12-93:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: existingLongReadAssembly (47:9-47:39)" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W002::Style/Medium] curly command found (34:5-44:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: javaPath (59:9-59:23)" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:21)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: keep (34:9-34:18)" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:30)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kmerCount (43:9-43:23)" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:33)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: linearSeqs (38:9-38:24)" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: long (31:9-31:19)" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:13-29:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lowScore (66:9-66:25)" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:16-31:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: makeblastdbPath (52:9-52:32)" +document = "biowdl/tasks:deconstructsigs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (47:14-47:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: maxKmerFrac (42:9-42:27)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W002::Style/Medium] curly command found (45:5-59:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory (69:9-69:31)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputGVCF (99:9-99:19)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minBridgeQual (37:9-37:29)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputGVCFIndex (100:9-100:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minComponentSize (62:9-62:30)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputVCF (96:9-96:18)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minDeadEndSize (63:9-63:28)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputVCFIndex (97:9-97:23)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minFastaLength (33:9-33:28)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputVCFStatsReport (98:9-98:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minKmerFrac (41:9-41:27)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:20)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minPolishSize (60:9-60:27)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mode (36:9-36:21)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:33)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: noCorrect (40:9-40:27)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:14-27:22)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: noMiniasm (45:9-45:27)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:14-28:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: noPilon (54:9-54:25)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:16-29:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: noRotate (48:9-48:26)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:16-30:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: out (25:9-25:19)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:17-31:45)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pilonPath (58:9-58:24)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:15-32:30)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preCommand (27:9-27:27)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:14-33:23)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: raconPath (46:9-46:24)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:17-34:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samtoolsPath (57:9-57:27)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:17-35:32)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: scores (65:9-65:23)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:17-37:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: short1 (28:9-28:21)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:18-38:32)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: short2 (29:9-29:21)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:13-41:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: spadesPath (39:9-39:25)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (42:16-42:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: startGeneCov (51:9-51:28)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (68:14-68:23)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: startGeneId (50:9-50:27)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (69:14-69:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: startGenes (49:9-49:25)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (70:21-70:41)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tblastnPath (53:9-53:26)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (71:15-71:25)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: threads (68:9-68:24)" +document = "biowdl/tasks:deepvariant.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (72:15-72:30)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unpaired (30:9-30:23)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W002::Style/Medium] curly command found (39:5-47:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (35:9-35:21)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: dellyBcf (74:9-74:17)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:unicycler.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: verbosity (32:9-32:23)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (106:14-106:23)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:vardict.wdl" -message = "[v1::W002::Style/Medium] curly command found (56:5-81:6)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (107:14-107:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:vardict.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: vcfFile (123:9-123:16)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:12)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:vt.wdl" -message = "[v1::W002::Style/Medium] curly command found (37:5-44:6)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:22-25:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:vt.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputVcf (69:9-69:18)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:22-26:30)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:whatshap.wdl" -message = "[v1::W002::Style/Medium] curly command found (118:5-126:6)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:14-27:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:whatshap.wdl" -message = "[v1::W002::Style/Medium] curly command found (178:5-189:6)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:14-28:31)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:whatshap.wdl" -message = "[v1::W002::Style/Medium] curly command found (47:5-63:6)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:16-29:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:whatshap.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: bam (218:9-218:12)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:15-31:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:whatshap.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: bamIndex (219:9-219:17)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:15-32:31)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:whatshap.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: phasedBlockList (155:9-155:24)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:13-35:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:whatshap.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: phasedGTF (153:9-153:18)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:16-36:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:whatshap.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: phasedTSV (154:9-154:18)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:14-50:22)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:whatshap.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: phasedVCF (97:9-97:18)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (51:14-51:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:whatshap.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: phasedVCFIndex (98:9-98:23)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (79:6-79:19)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W002::Style/Medium] curly command found (115:5-125:6)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (81:14-81:22)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W002::Style/Medium] curly command found (154:5-164:6)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (82:14-82:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W002::Style/Medium] curly command found (38:5-47:6)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (83:24-83:37)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W002::Style/Medium] curly command found (76:5-88:6)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (84:24-84:36)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binFile (108:9-108:22)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (85:16-85:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binFile (148:9-148:22)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (88:13-88:24)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binFile (32:9-32:22)" +document = "biowdl/tasks:delly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (89:16-89:27)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binFile (67:9-67:22)" +document = "biowdl/tasks:duphold.wdl" +message = "[v1::W002::Style/Medium] curly command found (38:5-47:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binSize (107:9-107:21)" +document = "biowdl/tasks:duphold.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputVcf (73:9-73:18)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binSize (147:9-147:21)" +document = "biowdl/tasks:duphold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:13)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binSize (31:9-31:21)" +document = "biowdl/tasks:duphold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:22)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binSize (66:9-66:21)" +document = "biowdl/tasks:duphold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:21)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dictionaryFile (143:9-143:28)" +document = "biowdl/tasks:duphold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:14-27:22)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dictionaryFileIndex (144:9-144:33)" +document = "biowdl/tasks:duphold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:14-28:28)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dockerImage (112:9-112:83)" +document = "biowdl/tasks:duphold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:14-29:31)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dockerImage (151:9-151:83)" +document = "biowdl/tasks:duphold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:16-31:26)" [[concerns]] kind 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missing parameter meta within task: fracN (68:9-68:21)" +document = "biowdl/tasks:extractSigPredictHRD.wdl" +message = "[v1::W002::Style/Medium] curly command found (38:5-45:6)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: inputBam (25:9-25:22)" +document = "biowdl/tasks:extractSigPredictHRD.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hg38 (31:9-31:29)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: inputBamIndex (26:9-26:27)" +document = "biowdl/tasks:extractSigPredictHRD.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:26)" [[concerns]] kind = "LintWarning" -document = "biowdl/tasks:wisestork.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: inputBed (141:9-141:22)" 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"[v1::W006::Naming/Low] identifier must be snake case (63:12-63:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (651:9-651:27)" +document = "biowdl/tasks:fastqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (93:14-93:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (702:9-702:27)" +document = "biowdl/tasks:fastqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (94:14-94:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (748:9-748:27)" +document = "biowdl/tasks:fastqc.wdl" 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within task: disk_size (927:8-927:26)" +document = "biowdl/tasks:fastqsplitter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dockerImage (36:9-36:89)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (996:9-996:27)" +document = "biowdl/tasks:fastqsplitter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: inputFastq (25:9-25:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (252:9-252:78)" +document = "biowdl/tasks:fastqsplitter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputPaths (26:9-26:35)" [[concerns]] kind = "LintWarning" -document = 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identifier must be snake case (29:14-29:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (747:9-747:78)" +document = "biowdl/tasks:fastqsplitter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:16-36:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (801:8-801:77)" +document = "biowdl/tasks:fastqsplitter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (59:11-59:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (864:9-864:78)" +document = "biowdl/tasks:fastqsplitter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (60:9-60:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (926:8-926:77)" +document = "biowdl/tasks:fgbio.wdl" +message = "[v1::W001::Style/Low] trailing space (36:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (995:9-995:78)" +document = "biowdl/tasks:fgbio.wdl" +message = "[v1::W001::Style/Low] trailing space (42:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image (167:5-167:80)" +document = "biowdl/tasks:fgbio.wdl" +message = "[v1::W002::Style/Medium] curly command 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"[v1::W003::Completeness/Medium] missing parameter meta within task: mem_size (652:9-652:26)" +document = "biowdl/tasks:flash.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minOverlap (33:9-33:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mem_size (703:9-703:26)" +document = "biowdl/tasks:flash.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outPrefix (29:9-29:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mem_size (749:9-749:26)" +document = "biowdl/tasks:flash.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outdirPath (28:9-28:26)" [[concerns]] kind = "LintWarning" -document = 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"biowdl/tasks:gatk.wdl" +message = "[v1::W001::Style/Low] trailing space (1635:59)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: plate_id (484:9-484:24)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (1009:5-1027:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: plate_id (545:9-545:24)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (107:5-123:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: plate_id (648:9-648:24)" +document = "biowdl/tasks:gatk.wdl" +message 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"[v1::W002::Style/Medium] curly command found (1258:5-1272:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: plate_id (856:9-856:24)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (1333:5-1344:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: plate_id (924:8-924:23)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (1401:5-1413:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: plate_id (993:9-993:24)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (1462:5-1474:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r1_adapter (242:9-242:26)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (1524:5-1534:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r1_hisat3n_stats (987:9-987:30)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (1584:5-1593:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r1_left_cut (244:9-244:24)" +document = "biowdl/tasks:gatk.wdl" +message = 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"[v1::W002::Style/Medium] curly command found (240:5-248:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r2_hisat3n_stats (988:9-988:30)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (287:5-294:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r2_left_cut (246:9-246:24)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (340:5-349:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r2_right_cut (247:9-247:25)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (398:5-409:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r2_trimmed_tar (319:9-319:28)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (42:5-54:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: random_primer_indexes (164:5-164:31)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (457:5-466:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: split_bam (698:9-698:23)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (588:5-596:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: split_fq_tar (542:9-542:26)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (637:5-647:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tarred_demultiplexed_fastqs (240:9-240:41)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W002::Style/Medium] curly command found (698:5-713:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tarred_index_files (320:9-320:32)" +document = "biowdl/tasks:gatk.wdl" 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: num_downstr_bases (23:9-23:34)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (103:13-103:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: num_upstr_bases (22:9-22:32)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (104:16-104:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: plate_id (9:9-9:24)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1071:6-1071:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r1_adapter (15:9-15:56)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1073:22-1073:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r1_left_cut (17:9-17:29)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1075:16-1075:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r1_right_cut (18:9-18:30)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1077:13-1077:24)" [[concerns]] kind 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[[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: extended_chip_manifest_file (75:5-75:38)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1446:14-1446:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_vcf_file (81:5-81:41)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1447:14-1447:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_vcf_index_file (82:5-82:47)" +document = 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(1506:6-1506:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: participant_id (37:5-37:27)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1508:14-1508:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: preemptible_tries (110:5-110:26)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1509:14-1509:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: product_family (53:5-53:27)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1510:14-1510:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: product_name (54:5-54:25)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1511:14-1511:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: product_order_id (55:5-55:29)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1512:14-1512:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/single_sample/Arrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: product_part_number 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(162:14-162:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: concordance_threshold (264:5-264:37)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1630:21-1630:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (266:5-266:18)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1631:21-1631:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_metrics_basename (262:5-262:35)" +document = 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parameter meta within task: truth_sample_name (261:5-261:29)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1636:23-1636:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_vcf_file (258:5-258:24)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1637:23-1637:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/arrays/validate_chip/ValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_vcf_index_file (259:5-259:30)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1639:17-1639:27)" [[concerns]] kind = "LintWarning" -document = 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf_index (22:5-22:25)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (196:14-196:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: eval_interval_list (36:5-36:28)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (228:6-228:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: excess_het_threshold (52:5-52:39)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (230:14-230:26)" [[concerns]] kind = 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workflow: excess_het_threshold (29:5-29:39)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (509:16-509:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gnarly_scatter_count (35:5-35:34)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (511:16-511:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gnarly_workaround (46:5-46:67)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (513:13-513:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gnarly_workaround_annotations (47:5-47:79)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (514:16-514:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gnarly_workaround_keys (48:5-48:40)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (542:14-542:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database (31:5-31:28)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (543:14-543:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: import_workaround (49:5-49:67)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (574:6-574:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: import_workaround_keys (50:5-50:40)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (576:16-576:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: large_disk (25:5-25:19)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (577:22-577:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: medium_disk (24:5-24:20)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (579:15-579:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (18:5-18:18)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (57:14-57:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (16:5-16:19)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (581:16-581:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: 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"broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: top_level_scatter_count (33:5-33:33)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (623:6-623:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unbounded_scatter_count_scale_factor (34:5-34:54)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (625:14-625:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unpadded_intervals_file (11:5-11:33)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (626:16-626:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_gnarly_genotyper (36:5-36:41)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (628:15-628:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: SNP_VQSR_downsampleFactor (61:5-61:34)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (629:15-629:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: annotation_db_vcf_indices_fofn (31:5-31:41)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (631:16-631:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: annotation_db_vcfs_fofn (30:5-30:34)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (633:13-633:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: axiomPoly_resource_vcf (51:5-51:32)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (634:16-634:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: axiomPoly_resource_vcf_index (52:5-52:38)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (650:14-650:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: callset_name (11:5-11:24)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (651:14-651:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_resource_vcf (53:5-53:40)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (677:6-677:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_resource_vcf_index (54:5-54:52)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (679:14-679:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf (18:5-18:19)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (680:14-680:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf_index (19:5-19:25)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (681:14-681:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: eval_interval_list (42:5-42:28)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (682:14-682:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: excess_het_threshold (58:5-58:39)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (683:14-683:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprinting_vcf_indices_fofn (33:5-33:41)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (684:16-684:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprinting_vcfs_fofn (32:5-32:34)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (685:13-685:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database (40:5-40:28)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (686:14-686:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hapmap_resource_vcf (43:5-43:29)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (688:15-688:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hapmap_resource_vcf_index (44:5-44:35)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (689:15-689:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hard_filtered_with_genotypes_vcf_indices_fofn (29:5-29:55)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (690:15-690:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hard_filtered_with_genotypes_vcfs_fofn (28:5-28:48)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (692:16-692:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: huge_disk (24:5-24:18)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (694:13-694:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: indel_filter_level (60:5-60:29)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (695:16-695:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: indel_recalibration_annotation_values (38:5-38:56)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (716:14-716:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: indel_recalibration_tranche_values (37:5-37:53)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (717:14-717:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: large_disk (23:5-23:19)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (718:14-718:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: medium_disk (22:5-22:20)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (753:6-753:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: mills_resource_vcf (49:5-49:28)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (755:21-755:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: mills_resource_vcf_index (50:5-50:34)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (756:16-756:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: omni_resource_vcf (45:5-45:27)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (758:13-758:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: omni_resource_vcf_index (46:5-46:33)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (759:13-759:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: one_thousand_genomes_resource_vcf (47:5-47:43)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (760:13-760:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: one_thousand_genomes_resource_vcf_index (48:5-48:49)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (761:16-761:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (16:5-16:18)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (774:14-774:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (14:5-14:19)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (797:6-797:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (15:5-15:25)" +document = "biowdl/tasks:gatk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (799:21-799:30)" [[concerns]] kind = "LintWarning" -document = 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"broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_disk_gb (602:5-602:31)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: filteredGff (91:9-91:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_disk_gb (99:9-99:35)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: proteinFasta (90:9-90:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_memory_mb (151:9-151:37)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_memory_mb (216:9-216:37)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_memory_mb (25:9-25:37)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_memory_mb (292:9-292:37)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:17-27:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_memory_mb (346:9-346:37)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:15-29:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_memory_mb (449:9-449:37)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:17-30:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_memory_mb (501:9-501:37)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:17-31:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_memory_mb (555:9-555:37)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:17-32:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_memory_mb (601:5-601:33)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:17-33:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_memory_mb (98:9-98:37)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:13-36:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assume_sort_order (393:5-393:43)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:16-37:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bams (386:5-386:22)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (61:15-61:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bqsr_recal_file (550:9-550:29)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (62:15-62:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: collate (80:9-80:24)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (63:15-63:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (389:5-389:30)" +document = "biowdl/tasks:gffread.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (64:15-64:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (150:9-150:20)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W002::Style/Medium] curly command found (213:5-225:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (215:9-215:20)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W002::Style/Medium] curly command found (275:5-297:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (24:9-24:20)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W002::Style/Medium] curly command found (352:5-359:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (289:9-289:21)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W002::Style/Medium] curly command found (401:5-411:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (343:9-343:21)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W002::Style/Medium] curly command found (41:5-51:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (446:9-446:20)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W002::Style/Medium] curly command found (457:5-469:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (498:9-498:20)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: assembly (335:9-335:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (552:9-552:20)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: assemblyIndex (336:9-336:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (95:9-95:20)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: vcf (333:9-333:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: emit_original_quals (551:9-551:43)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: vcfIndex (334:9-334:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: exclude (81:9-81:58)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: referenceFastaDict (446:9-446:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq1_suffix (147:9-147:42)" - +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: referenceFastaFai (445:9-445:31)" + [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq_o1_suffix (210:9-210:45)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: threads (34:9-34:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq_o2_suffix (211:9-211:45)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcfIndexes (201:9-201:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq_record (280:9-280:37)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (135:15-135:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq_record (334:9-334:39)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (155:6-155:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq_s_suffix (212:9-212:43)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (157:14-157:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: filename (82:9-82:22)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (158:14-158:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gz (83:9-83:19)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (159:13-159:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (444:9-444:23)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (160:16-160:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (599:5-599:19)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (163:16-163:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: inputformat (84:9-84:35)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (164:13-164:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: level (85:9-85:22)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (198:6-198:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (149:9-149:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (200:22-200:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (214:9-214:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (201:22-201:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (23:9-23:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (202:14-202:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (291:9-291:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (203:14-203:31)" [[concerns]] kind = "LintWarning" 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task: max_retries (448:9-448:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (209:16-209:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (500:9-500:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (210:13-210:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (554:9-554:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (254:6-254:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (97:9-97:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (256:22-256:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (399:5-399:30)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (257:22-257:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outbam (387:5-387:18)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (258:24-258:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_prefix (600:5-600:29)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:6-25:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputdir (86:9-86:31)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (260:16-260:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputperreadgroup (87:9-87:35)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (262:15-262:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputperreadgroupsuffixF (88:9-88:54)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (263:15-263:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputperreadgroupsuffixF2 (89:9-89:55)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (264:17-264:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputperreadgroupsuffixO (90:9-90:55)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (265:15-265:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputperreadgroupsuffixO2 (91:9-91:56)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (266:15-266:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputperreadgroupsuffixS (92:9-92:54)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (268:13-268:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (148:9-148:29)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (269:13-269:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (213:9-213:29)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (271:13-271:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (22:9-22:29)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (272:16-272:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (290:9-290:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:14-27:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (344:9-344:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:16-28:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (447:9-447:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:14-29:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (499:9-499:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (301:14-301:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (553:9-553:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (303:14-303:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (96:9-96:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:14-30:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (390:5-390:30)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:14-31:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_name_regex (398:5-398:28)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:14-32:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: readgroups (146:9-146:34)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (340:6-340:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: readgroups (209:9-209:34)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (342:14-342:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_amb (284:9-284:21)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (343:14-343:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_amb (337:9-337:21)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (344:16-344:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_ann (285:9-285:21)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (348:16-348:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_ann (338:9-338:21)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (349:13-349:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_bwt (286:9-286:21)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:16-35:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_bwt (339:9-339:21)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (362:14-362:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (283:9-283:22)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (363:14-363:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (336:9-336:22)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:16-37:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fai (282:9-282:21)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (385:6-385:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fai (342:9-342:21)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (387:14-387:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (281:9-281:23)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (388:14-388:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (335:9-335:23)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (389:14-389:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_pac (287:9-287:21)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:13-38:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_pac (340:9-340:21)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (390:14-390:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_sa (288:9-288:20)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (391:16-391:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_sa (341:9-341:20)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (392:16-392:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sorting_collection_size_ratio (402:5-402:41)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (395:16-395:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tmp_prefix (445:9-445:38)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (396:13-396:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tryoq (93:9-93:22)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (399:12-399:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: validation_stringency (392:5-392:44)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (414:14-414:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (639:9-639:30)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (415:14-415:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_vcf (643:9-643:31)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (416:14-416:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_vcf_index (644:9-644:37)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (417:14-417:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing 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kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf_index (646:9-646:29)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (445:14-445:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (634:9-634:24)" +document = "biowdl/tasks:gridss.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (446:14-446:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] 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"broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W001::Style/Low] trailing space (52:58)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1057:16-1057:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W001::Style/Low] trailing space (54:61)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1058:22-1058:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W001::Style/Low] trailing space (55:52)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1059:22-1059:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W001::Style/Low] trailing space (56:60)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (105:16-105:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W001::Style/Low] trailing space (57:54)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1060:14-1060:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chip_well_barcode (20:9-20:34)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1061:14-1061:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbSNP_vcf (30:9-30:26)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1062:14-1062:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbSNP_vcf_index (31:9-31:32)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1063:14-1063:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: disk_size (34:9-34:26)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1064:14-1064:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: environment (36:9-36:28)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1065:14-1065:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: green_idat_cloud_path (26:9-26:38)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1066:14-1066:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database_file (32:9-32:40)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1067:14-1067:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lab_batch (24:9-24:26)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1068:14-1068:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: preemptible_tries (35:9-35:34)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1069:14-1069:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: red_idat_cloud_path (25:9-25:36)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (106:14-106:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (29:9-29:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1070:14-1070:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (27:9-27:26)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1071:14-1071:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (28:9-28:32)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1072:14-1072:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reported_gender (23:9-23:32)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1073:16-1073:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_alias (21:9-21:29)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1074:16-1074:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_lsid (22:9-22:28)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1076:14-1076:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tdr_dataset_id (16:9-16:31)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1077:14-1077:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tdr_target_table_name (17:9-17:38)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1078:14-1078:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: variant_rsids_file (33:9-33:35)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1079:14-1079:32)" [[concerns]] kind = "LintWarning" -document = 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= "[v1::W006::Naming/Low] identifier must be snake case (1084:16-1084:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (19:1-19:2)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1086:16-1086:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (21:1-21:2)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (108:16-108:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (289:1-289:2)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (109:14-109:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (294:1-294:6)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (110:14-110:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (72:1-72:2)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1114:14-1114:38)" [[concerns]] kind = "LintWarning" -document = 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"[v1::W003::Completeness/Medium] missing parameter meta within task: agg_gc_bias_detail_metrics (319:7-319:40)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1117:14-1117:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: agg_gc_bias_pdf (320:7-320:29)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1118:14-1118:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: agg_gc_bias_summary_metrics (321:7-321:41)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1119:14-1119:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: agg_quality_distribution_metrics (323:7-323:46)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (111:16-111:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: agg_quality_distribution_pdf (322:7-322:42)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1120:14-1120:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: alignment_summary_metrics (199:5-199:35)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1121:14-1121:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: barcode (330:7-330:21)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1122:14-1122:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing 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(1125:14-1125:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_metrics (204:5-204:31)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1126:14-1126:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (209:5-209:16)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1127:14-1127:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (338:7-338:18)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1128:14-1128:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (424:7-424:18)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1129:14-1129:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (211:5-211:26)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (112:14-112:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (340:7-340:28)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1130:14-1130:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (426:7-426:28)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1131:14-1131:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (208:5-208:39)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1132:14-1132:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_metrics (201:5-201:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1133:14-1133:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_metrics (316:7-316:31)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1134:14-1134:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplication_rate (324:7-324:29)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1135:14-1135:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: filtered_vcf (310:7-310:26)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1136:14-1136:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: filtered_vcf_index (311:7-311:32)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1137:14-1137:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fingerprint_detail_metrics_file (333:7-333:51)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1138:14-1138:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fingerprint_summary_metrics (205:5-205:38)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1139:14-1139:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fingerprint_summary_metrics_file (334:7-334:52)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1140:15-1140:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: flow_order (329:7-329:24)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1141:14-1141:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gc_bias_summary_metrics (200:5-200:33)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1142:14-1142:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: haplotype_bam (300:7-300:33)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1143:14-1143:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: haplotype_bam_index (301:7-301:39)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1144:14-1144:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: id (331:7-331:16)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1145:14-1145:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: is_outlier_data (326:7-326:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1146:14-1146:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (210:5-210:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1147:14-1147:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (339:7-339:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1148:14-1148:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (425:7-425:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1149:14-1149:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (206:5-206:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1150:14-1150:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (292:7-292:29)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1151:14-1151:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_cram (303:7-303:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (116:16-116:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_cram_index (304:7-304:31)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (117:13-117:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_cram_md5 (305:7-305:29)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (118:16-118:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_gvcf (295:7-295:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1207:6-1207:10)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_gvcf_index (296:7-296:31)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1209:16-1209:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf (297:7-297:24)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1210:14-1210:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf_index (298:7-298:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1211:14-1211:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputs_json (422:7-422:24)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1212:14-1212:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: quality_yield_metrics (202:5-202:31)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1213:14-1213:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: quality_yield_metrics (313:7-313:35)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1214:14-1214:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: raw_wgs_metrics (203:5-203:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1216:14-1216:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: raw_wgs_metrics (315:7-315:29)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1217:14-1217:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_name (328:7-328:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1218:17-1218:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: selfSM (307:7-307:20)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1219:17-1219:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tdr_dataset_uuid (421:7-421:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1220:16-1220:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unified_metrics (336:7-336:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1222:17-1222:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wgs_metrics (198:5-198:21)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1223:15-1223:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wgs_metrics (314:7-314:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1224:15-1224:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: alignment_references (24:3-24:43)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1225:14-1225:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: collab_sample_id_run_id (39:3-39:33)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1226:14-1226:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_sites (23:3-23:41)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1227:14-1227:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: filtering_model_no_gt_name (37:3-37:74)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1228:14-1228:46)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database_file (17:3-17:129)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1229:14-1229:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam_list (30:3-30:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1230:14-1230:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: make_haplotype_bam (35:3-35:37)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1231:17-1231:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: merge_bam_file (34:3-34:32)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1232:15-1232:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reads_per_split (36:3-36:33)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1235:16-1235:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rsq_threshold (33:3-33:28)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1237:13-1237:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: variant_calling_settings (25:3-25:50)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1238:16-1238:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vcf_post_processing (26:3-26:40)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1266:14-1266:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: allow_lod_zero (54:5-54:35)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1267:14-1267:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: environment (56:5-56:24)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1268:15-1268:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_vcf (41:5-41:36)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1269:15-1269:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_vcf_index (42:5-42:42)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1270:14-1270:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database_file (53:5-53:33)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1271:14-1271:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (32:5-32:20)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1272:14-1272:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam_index (33:5-33:26)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1313:6-1313:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_sample_alias (36:5-36:31)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1315:16-1315:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_vcf (30:5-30:20)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1316:14-1316:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_vcf_index (31:5-31:26)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1317:14-1317:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_basename (47:5-47:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1318:14-1318:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read_fingerprint_from_mercury (40:5-40:50)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1319:14-1319:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (51:5-51:18)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1320:14-1320:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (49:5-49:19)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1321:14-1321:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (50:5-50:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1322:16-1322:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_alias (45:5-45:24)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1325:16-1325:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_lsid (44:5-44:24)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1326:13-1326:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (57:5-57:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1327:16-1327:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cram_file (143:5-143:19)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1343:14-1343:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (103:5-103:18)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (134:14-134:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (145:5-145:18)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (135:14-135:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (179:5-179:18)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (136:14-136:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (212:5-212:23)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (137:14-137:30)" [[concerns]] kind = 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"biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (209:15-209:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_in_MiB (241:5-241:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (210:14-210:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_in_MiB (269:5-269:29)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (231:6-231:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" 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"broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rg_to_ubam_file (239:5-239:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (241:14-241:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sort_sam_disk_multiplier (303:5-303:39)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (242:16-242:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unmapped_bam_suffix (178:5-178:31)" +document = 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"[v1::W003::Completeness/Medium] missing parameter meta within task: fwd_converted_reference_fasta (563:7-563:41)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (644:14-644:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mapped_bam_input (647:7-647:28)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (645:14-645:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mem_size_gib (1085:7-1085:31)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (646:14-646:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: methylation_vcf_output_name (1083:7-1083:39)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (64:14-64:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_length (388:7-388:21)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (65:14-65:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_map_quality (854:7-854:26)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (66:14-66:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (1033:7-1033:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (67:14-67:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (1118:7-1118:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (685:6-685:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (1159:7-1159:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (687:16-687:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (398:7-398:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (689:16-689:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (456:7-456:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (690:22-690:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (508:7-508:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (691:17-691:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (568:7-568:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (694:16-694:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (653:7-653:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (695:13-695:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (711:7-711:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (696:16-696:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (757:7-757:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (741:6-741:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (806:7-806:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (743:16-743:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (856:7-856:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (744:14-744:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (906:7-906:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (745:23-745:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (980:7-980:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (746:16-746:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (1032:7-1032:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (747:16-747:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (1158:7-1158:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (748:14-748:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (393:7-393:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (749:14-749:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (455:7-455:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (750:14-750:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (507:7-507:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (751:14-751:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (567:7-567:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (752:14-752:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (652:7-652:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (753:14-753:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (710:7-710:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (754:14-754:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (756:7-756:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (755:14-755:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (805:7-805:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (756:14-756:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (855:7-855:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (757:14-757:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (905:7-905:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (758:14-758:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (979:7-979:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (759:22-759:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: paired_end_run (557:7-557:29)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (760:14-760:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: quality_cutoff (396:7-396:26)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (761:14-761:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read1_adapter_seq (394:7-394:32)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (762:14-762:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read2_adapter_seq (395:7-395:32)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (763:14-763:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" 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= "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_group_platform_unit_name (977:7-977:43)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (767:14-767:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_dictionary (1031:7-1031:32)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (768:14-768:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_dictionary (650:7-650:32)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (769:22-769:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_fasta (1029:7-1029:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (770:14-770:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_fasta (1117:7-1117:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (771:14-771:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_fasta (561:7-561:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (772:15-772:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_fasta (649:7-649:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (773:14-773:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_fasta_index (1030:7-1030:33)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (774:14-774:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_fasta_index (562:7-562:33)" 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within task: rev_converted_reference_fasta (565:7-565:41)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (779:14-779:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tagged_unmapped_bam_input (648:7-648:37)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (782:16-782:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unmapped_bam_input (503:7-503:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (783:13-783:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: barcode_length (20:7-20:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (784:16-784:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: barcode_start_pos (19:7-19:28)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (830:14-830:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: barcode_white_list (16:7-16:31)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (831:14-831:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cut_length (39:7-39:21)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (886:6-886:10)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: extract_and_attach_barcodes_in_single_end_run (48:7-48:60)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (888:16-888:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_r1_gzipped_input (10:7-10:34)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (889:16-889:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_r2_gzipped_input (11:7-11:34)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (890:14-890:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fwd_bowtie2_index_files (30:7-30:42)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (891:14-891:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fwd_converted_reference_fasta (28:7-28:41)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (892:14-892:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_length_paired_end_trim (35:7-35:37)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (893:14-893:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_length_single_end_trim (36:7-36:37)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (894:14-894:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_map_quality (51:7-51:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (895:16-895:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: monitoring_script (13:7-13:30)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (896:14-896:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_base_sample_name (7:7-7:37)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (898:14-898:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: paired_end_run (42:7-42:29)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (899:14-899:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: quality_cutoff (34:7-34:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (900:14-900:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read1_adapter_seq (37:7-37:31)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (901:14-901:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read2_adapter_seq (38:7-38:31)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (903:13-903:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read_group_library_name (54:7-54:53)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (904:16-904:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read_group_platform_name (55:7-55:51)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (906:16-906:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read_group_platform_unit_name (56:7-56:56)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (923:14-923:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_dictionary (27:7-27:32)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (924:14-924:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_fasta (25:7-25:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (958:6-958:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_fasta_index (26:7-26:33)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (960:16-960:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: remove_duplicates (45:7-45:32)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (961:16-961:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rev_bowtie2_index_files (31:7-31:42)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (962:16-962:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rev_converted_reference_fasta (29:7-29:41)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (963:24-963:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotation_gtf (92:5-92:24)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (964:16-964:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: biotypes (93:5-93:18)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (965:22-965:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chrom_sizes_file (157:5-157:27)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (966:14-966:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (94:5-94:19)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (967:14-967:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genome_build (164:5-164:24)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (968:14-968:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genome_build (88:5-88:24)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (969:14-969:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genome_fa (156:5-156:19)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (970:14-970:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genome_fa (63:5-63:19)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (971:14-971:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genome_fa (91:5-91:19)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (972:14-972:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genome_source (162:5-162:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (973:14-973:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genome_source (86:5-86:25)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (974:14-974:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gtf_annotation_version (160:5-160:34)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (975:14-975:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gtf_annotation_version (84:5-84:34)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (976:14-976:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: organism (166:5-166:20)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (977:14-977:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: organism (90:5-90:20)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (978:14-978:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/build_indices/BuildIndices.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: organism (11:5-11:20)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (984:13-984:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (118:1-118:8)" +document = "biowdl/tasks:hmftools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (985:16-985:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W001::Style/Low] trailing space (18:41)" +document = "biowdl/tasks:htseq.wdl" +message = "[v1::W002::Style/Medium] curly command found (41:5-54:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: 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missing parameter meta within workflow: atac_r1_fastq (33:9-33:34)" +document = "biowdl/tasks:htseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_r2_fastq (34:9-34:34)" +document = "biowdl/tasks:htseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_r3_fastq (35:9-35:34)" +document = "biowdl/tasks:htseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:23-30:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_whitelist (43:9-43:113)" +document = "biowdl/tasks:htseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:17-32:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chrom_sizes (38:9-38:25)" +document = "biowdl/tasks:htseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:13-37:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: count_exons (28:9-28:36)" +document = "biowdl/tasks:htseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:16-38:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: counting_mode (15:9-15:40)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W002::Style/Medium] curly command found (40:5-52:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: emptydrops_lower (24:9-24:35)" - +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: refineBam (86:9-86:18)" + [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: force_no_check (25:9-25:39)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: refineBamIndex (87:9-87:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gex_i1_fastq (18:9-18:34)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: refineConsensusReadset (88:9-88:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gex_r1_fastq (16:9-16:33)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: refineFilterSummary (89:9-89:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gex_r2_fastq (17:9-17:33)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: refineReport (90:9-90:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gex_whitelist (29:9-29:111)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: refineStderr (91:9-91:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ignore_r1_read_length (26:9-26:46)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within 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within workflow: run_cellbender (46:9-46:39)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:14-28:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: star_strand_mode (27:9-27:44)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:14-29:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tar_bwa_reference (37:9-37:31)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:14-30:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tar_star_reference (19:9-19:32)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:16-31:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/Multiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tenx_chemistry_version (23:9-23:39)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:16-32:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/atac.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (211:1-211:4)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:13-36:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/atac.wdl" -message = "[v1::W001::Style/Low] line contains only 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"[v1::W006::Naming/Low] identifier must be snake case (57:14-57:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/atac.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (245:1-245:4)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (58:14-58:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/atac.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (248:1-248:4)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (59:14-59:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/atac.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (252:1-252:4)" +document = "biowdl/tasks:isoseq3.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (60:14-60:26)" [[concerns]] kind = 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"[v1::W001::Style/Low] trailing space (288:68)" +document = "biowdl/tasks:lima.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (100:21-100:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/atac.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within workflow: output_base_name (44:5-44:21)" +document = "biowdl/tasks:lima.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (101:14-101:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/atac.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpuPlatform (317:5-317:46)" +document = "biowdl/tasks:lima.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (102:14-102:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/multiome/atac.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter 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within workflow: annotations_gtf (19:9-19:29)" +document = "biowdl/tasks:lima.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (54:16-54:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/paired_tag/PairedTag.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_r1_fastq (32:9-32:34)" +document = "biowdl/tasks:lima.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (57:25-57:45)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/paired_tag/PairedTag.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_r2_fastq (33:9-33:34)" +document = "biowdl/tasks:lima.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (98:21-98:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/paired_tag/PairedTag.wdl" -message = "[v1::W003::Completeness/Medium] missing 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missing parameter meta within workflow: count_exons (27:9-27:36)" +document = "biowdl/tasks:macs2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:22-25:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/paired_tag/PairedTag.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: counting_mode (14:9-14:40)" +document = "biowdl/tasks:macs2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:22-26:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/paired_tag/PairedTag.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: emptydrops_lower (23:9-23:35)" +document = "biowdl/tasks:macs2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:21-27:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/paired_tag/PairedTag.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: force_no_check (24:9-24:39)" +document = "biowdl/tasks:macs2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:21-28:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/paired_tag/PairedTag.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gex_i1_fastq (17:9-17:34)" +document = "biowdl/tasks:macs2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:16-29:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/paired_tag/PairedTag.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gex_r1_fastq (15:9-15:33)" +document = "biowdl/tasks:macs2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:16-30:26)" [[concerns]] kind = "LintWarning" -document = 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"LintWarning" -document = "broadinstitute/warp:pipelines/skylab/paired_tag/PairedTag.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id (11:9-11:24)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W002::Style/Medium] curly command found (109:5-122:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/paired_tag/PairedTag.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: mt_genes (21:9-21:23)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W002::Style/Medium] curly command found (41:5-54:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/paired_tag/PairedTag.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: preindex (45:9-45:32)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: candidatSVVcfIndex 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: annotations_gtf (36:9-36:29)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (104:13-104:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bead_locations (40:9-40:28)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (105:13-105:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/slideseq/SlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: count_exons (39:9-39:35)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (106:16-106:27)" [[concerns]] kind = "LintWarning" -document = 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"broadinstitute/warp:pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: project_name (35:7-35:34)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (91:14-91:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: species (37:7-37:29)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (92:14-92:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (37:1-37:2)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (93:14-93:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (22:1-22:2)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (94:14-94:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chromosome_sizes (135:5-135:26)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (95:16-95:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (140:5-140:24)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (98:15-98:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (60:5-60:23)" +document = "biowdl/tasks:manta.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (99:15-99:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image (139:5-139:80)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W002::Style/Medium] curly command found (106:5-126:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image (59:5-59:80)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W002::Style/Medium] curly command found (39:5-50:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq_input_read1 (54:5-54:34)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: alignmentFile (162:9-162:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq_input_read2 (55:5-55:34)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: indexFile (77:9-77:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genome_fa (136:5-136:19)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (102:13-102:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mapping_yaml (133:5-133:22)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (103:16-103:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mem_size (141:5-141:23)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (129:14-129:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mem_size (61:5-61:22)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake 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(27:13-27:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: snakefile (134:5-134:19)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:16-28:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tarred_demultiplexed_fastqs (131:5-131:37)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:14-29:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tarred_index_files (132:5-132:28)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:14-31:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chromosome_sizes (17:5-17:26)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:13-35:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_input_read1 (7:5-7:34)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:16-36:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_input_read2 (8:5-8:34)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (53:14-53:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genome_fa (18:5-18:19)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (81:6-81:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: mapping_yaml (15:5-15:22)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (83:16-83:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_basename (11:5-11:38)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (84:13-84:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: plate_id (10:5-10:20)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (85:17-85:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: random_primer_indexes (9:5-9:31)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (86:17-86:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: snakefile (16:5-16:19)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (87:16-87:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:pipelines/skylab/snM3C/snM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tarred_index_files (14:5-14:28)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (88:17-88:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (29:1-29:4)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (89:17-89:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: all_libraries (24:5-24:32)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (90:14-90:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: all_organs (25:5-25:29)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (91:14-91:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: all_project_ids (27:5-27:34)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (93:14-93:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: all_project_names (28:5-28:36)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (94:14-94:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: all_species (26:5-26:30)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (95:14-95:42)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cromwell_url (35:5-35:55)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (96:14-96:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_1_uuids (19:5-19:32)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (97:14-97:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_2_uuids (20:5-20:32)" +document = "biowdl/tasks:minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (98:17-98:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_i1_uuids (21:5-21:34)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (89:1-89:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_ids (18:5-18:28)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W001::Style/Low] trailing space (72:70)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: is_update (31:5-31:22)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W001::Style/Low] trailing space (75:78)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_bams (16:5-16:28)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W001::Style/Low] trailing space (76:78)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_basename (33:5-33:27)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W001::Style/Low] trailing space (77:78)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_looms (17:5-17:29)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W001::Style/Low] trailing space (84:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: pipeline_type (37:5-37:37)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W002::Style/Medium] curly command found (81:5-130:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: staging_area (36:5-36:69)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (132:12-132:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: version_timestamp (40:5-40:30)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (137:14-137:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: workspace_bucket (38:5-38:28)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (138:15-138:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bam (12:5-12:14)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cromwell_url (18:5-18:24)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:17-30:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id (15:5-15:20)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:16-31:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: is_project_level (19:5-19:29)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:17-32:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: loom (13:5-13:14)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:17-33:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: pipeline_version (20:5-20:29)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:17-41:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: process_input_ids (14:5-14:36)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (43:14-43:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: project_id (16:5-16:22)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (46:17-46:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_file_fasta (21:5-21:33)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:17-50:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/CreateOptimusAdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: version_timestamp (17:5-17:29)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (51:15-51:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/MergeOptimusLooms.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: library (15:5-15:19)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (52:15-52:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/MergeOptimusLooms.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: organ (17:5-17:17)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (55:17-55:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/MergeOptimusLooms.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_basename (20:5-20:27)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (57:17-57:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/MergeOptimusLooms.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_looms (14:5-14:29)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (60:13-60:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/MergeOptimusLooms.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: project_id (18:5-18:22)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (61:16-61:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/MergeOptimusLooms.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: project_name (19:5-19:24)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (64:9-64:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/optimus/MergeOptimusLooms.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: species (16:5-16:19)" +document = "biowdl/tasks:multiqc.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (69:12-69:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: all_libraries (23:5-23:32)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W002::Style/Medium] curly command found (138:5-146:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: all_organs (24:5-24:29)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W002::Style/Medium] curly command found (50:5-67:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: all_project_ids (26:5-26:34)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: dynamicHistogram (112:9-112:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: all_project_names (27:5-27:36)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: lengthVsQualityScatterPlotDot (119:9-119:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: all_species (25:5-25:30)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: lengthVsQualityScatterPlotKde (120:9-120:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cromwell_url (32:5-32:55)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: log (171:9-171:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_1_uuids (19:5-19:32)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: logScaleReadLengthHistogram (114:9-114:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_2_uuids (20:5-20:33)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: readLengthHistogram (113:9-113:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_ids (18:5-18:28)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: report (115:9-115:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: is_update (30:5-30:22)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: report (170:9-170:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_bais (16:5-16:28)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: stats (121:9-121:14)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_bams (15:5-15:28)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: weightedHistogram (116:9-116:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_loom (17:5-17:21)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: weightedLogScaleHistogram (117:9-117:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: pipeline_type (34:5-34:33)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: yieldByLength (118:9-118:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: staging_area (33:5-33:69)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (125:6-125:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: version_timestamp (37:5-37:30)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (127:14-127:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: workspace_bucket (35:5-35:28)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (128:16-128:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W001::Style/Low] trailing space (20:28)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (129:17-129:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W001::Style/Low] trailing space (21:32)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (131:14-131:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bai (13:5-13:14)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (134:13-134:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bam (12:5-12:14)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (135:16-135:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id (16:5-16:20)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:14)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: is_project_level (19:5-19:29)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: loom (14:5-14:15)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:16-26:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: metadata (22:5-22:18)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: pipeline_type (18:5-18:25)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:16-28:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: pipeline_version (20:5-20:28)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:16-29:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_file_fasta (21:5-21:32)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:17-30:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ss2_index (15:5-15:19)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:17-31:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/smartseq2/CreateSs2AdapterObjects.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: version_timestamp (17:5-17:29)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:17-32:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (329:1-329:4)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:17-34:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (591:1-591:6)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:14-37:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (602:1-602:2)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:14-38:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (614:1-614:2)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (39:14-39:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W001::Style/Low] trailing space (345:39)" +document = "biowdl/tasks:nanopack.wdl" +message = 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(425:3-436:4)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (74:14-74:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (488:3-492:4)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (75:14-75:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (519:3-523:4)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (76:14-76:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (551:3-554:4)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (77:15-77:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (653:3-655:4)" +document = "biowdl/tasks:nanopack.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (78:15-78:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (746:3-752:6)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W002::Style/Medium] curly command found (104:5-114:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (74:3-84:4)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W002::Style/Medium] curly command found (132:5-146:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: analysis_file_descriptor_objects (573:5-573:51)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W002::Style/Medium] curly command found (43:5-77:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: analysis_file_metadata_objects (570:5-570:49)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assemblyLevel (32:9-32:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: analysis_process_objects (571:5-571:43)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: debug (27:9-27:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: analysis_process_path (277:5-277:38)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: domain (39:9-39:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: analysis_process_path_list (281:5-281:46)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: downloadDir (128:9-128:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: analysis_protocol_objects (572:5-572:44)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: executable (28:9-28:51)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: analysis_protocol_path (278:5-278:39)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: format (31:9-31:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: analysis_protocol_path_list (282:5-282:47)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gzip (129:9-129:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_type (412:5-412:25)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: humanReadable (35:9-35:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bai_array (284:5-284:29)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: libraryPath (97:9-97:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam_array (283:5-283:29)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ncbiBaseUri (36:9-36:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bucket_path (671:5-671:23)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ntDir (100:9-100:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cache_invalidate (580:5-580:29)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ntFilePath (101:9-101:46)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (110:5-110:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputPath (25:9-25:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (14:5-14:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: parallel (37:9-37:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (150:5-150:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preCommand (40:9-40:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (204:5-204:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refseqCategory (34:9-34:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (242:5-242:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: retries (38:9-38:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (289:5-289:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: section (30:9-30:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (372:5-372:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: seqTaxMapPath (98:9-98:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (420:5-420:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxId (33:9-33:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (456:5-456:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unzip (99:9-99:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (483:5-483:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: verbose (26:9-26:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (514:5-514:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W005::Completeness/Medium] missing runtime block within a task (126:1-152:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (546:5-546:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W005::Completeness/Medium] missing runtime block within a task (23:1-92:3)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (583:5-583:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W005::Completeness/Medium] missing runtime block within a task (95:1-124:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (648:5-648:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (100:16-100:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (674:5-674:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (101:16-101:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (69:5-69:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (117:14-117:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (709:5-709:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (121:21-121:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (741:5-741:16)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (122:21-122:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: creation_time (366:5-366:25)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (126:6-126:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cromwell_metadata (479:5-479:27)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (128:16-128:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cromwell_url (64:5-64:24)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (149:21-149:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: data_objects (575:5-575:31)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (150:21-150:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (112:5-112:66)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (152:5-152:88)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:16-25:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (16:5-16:25)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:17-32:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (206:5-206:59)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:17-33:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (244:5-244:25)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:17-34:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (291:5-291:59)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:18-35:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (374:5-374:56)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:17-36:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (422:5-422:25)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (40:17-40:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (458:5-458:25)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (80:21-80:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (485:5-485:60)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (81:21-81:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (516:5-516:62)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (82:21-82:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (548:5-548:80)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (83:21-83:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (585:5-585:26)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (84:21-84:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (650:5-650:25)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (85:21-85:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (676:5-676:25)" +document = "biowdl/tasks:ncbi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (86:21-86:31)" [[concerns]] kind = "LintWarning" -document = 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"broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (582:5-582:82)" +document = "biowdl/tasks:pacbio.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (61:6-61:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (647:5-647:35)" +document = "biowdl/tasks:pacbio.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (63:13-63:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (673:5-673:82)" +document = "biowdl/tasks:pacbio.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (66:16-66:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (68:5-68:82)" +document = "biowdl/tasks:pbbam.wdl" +message = "[v1::W002::Style/Medium] curly command found (38:5-47:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (708:5-708:82)" +document = "biowdl/tasks:pbbam.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: index (70:9-70:14)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (740:5-740:82)" +document = "biowdl/tasks:pbbam.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: indexedBam (69:9-69:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: done (738:5-738:17)" +document = "biowdl/tasks:pbbam.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq1_array (285:5-285:32)" +document = "biowdl/tasks:pbbam.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq2_array (286:5-286:32)" +document = "biowdl/tasks:pbbam.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:17-27:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_name_string (274:5-274:28)" +document = "biowdl/tasks:pbbam.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:13-30:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_path (369:5-369:19)" +document = "biowdl/tasks:pbbam.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:16-31:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_path (409:5-409:21)" +document = "biowdl/tasks:pbbam.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:12-35:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_path (453:5-453:21)" +document = "biowdl/tasks:pbbam.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:12-36:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_path_string (368:5-368:28)" +document = "biowdl/tasks:pbbam.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:14-50:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genus_species (411:5-411:25)" +document = "biowdl/tasks:pbmm2.wdl" +message = "[v1::W002::Style/Medium] curly command found (37:5-46:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: illegal_characters (11:5-11:35)" +document = "biowdl/tasks:pbmm2.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputAlignmentFile (73:9-73:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: include_keys (66:5-66:25)" +document = "biowdl/tasks:pbmm2.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputIndexFile (74:9-74:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: include_subworkflows (65:5-65:41)" +document = "biowdl/tasks:pbmm2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_array (9:5-9:30)" +document = "biowdl/tasks:pbmm2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:16-25:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (144:5-144:21)" +document = "biowdl/tasks:pbmm2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:14-28:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (199:5-199:20)" +document = "biowdl/tasks:pbmm2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:14-29:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_type (10:5-10:22)" +document = "biowdl/tasks:pbmm2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:13-33:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_uuid (140:5-140:22)" +document = "biowdl/tasks:pbmm2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:16-34:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_uuid (195:5-195:22)" +document = "biowdl/tasks:pbmm2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (49:14-49:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_uuid (235:5-235:22)" +document = "biowdl/tasks:pbmm2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:14-50:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_uuid (364:5-364:22)" +document = "biowdl/tasks:peach.wdl" +message = "[v1::W002::Style/Medium] curly command found (37:5-47:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_uuid (410:5-410:22)" +document = "biowdl/tasks:peach.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: intermediate_analysis_files (543:5-543:44)" +document = "biowdl/tasks:peach.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: is_update (706:5-706:22)" +document = "biowdl/tasks:peach.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: is_update_file (578:5-578:26)" +document = "biowdl/tasks:peach.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: library (102:5-102:19)" +document = "biowdl/tasks:peach.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:16-28:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: links_objects (574:5-574:32)" +document = "biowdl/tasks:peach.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:16-29:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (111:5-111:66)" +document = "biowdl/tasks:peach.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:14-30:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (151:5-151:88)" +document = "biowdl/tasks:peach.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:16-33:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (15:5-15:25)" +document = "biowdl/tasks:peach.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:13-34:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (205:5-205:59)" +document = "biowdl/tasks:peach.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:14-50:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (243:5-243:25)" +document = "biowdl/tasks:peach.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (51:14-51:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (290:5-290:56)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (1220:1-1220:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (373:5-373:56)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (174:1-174:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (421:5-421:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (509:1-509:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (457:5-457:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (543:1-543:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (484:5-484:59)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (739:1-739:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (515:5-515:62)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W001::Style/Low] trailing space (832:85)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (547:5-547:80)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (1002:5-1017:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (584:5-584:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (1065:5-1073:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (649:5-649:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (1114:5-1122:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (675:5-675:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (1169:5-1187:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (70:5-70:53)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (153:5-162:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (710:5-710:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (216:5-233:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (742:5-742:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (342:5-352:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ncbi_taxon_id (414:5-414:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (35:5-43:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: organ (104:5-104:17)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (400:5-412:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (107:5-107:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (462:5-470:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_file_path (272:5-272:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (520:5-532:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_looms (101:5-101:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (575:5-583:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_path (63:5-63:23)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (627:5-639:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (141:5-141:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (690:5-701:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (196:5-196:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (763:5-781:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (236:5-236:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (844:5-854:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (271:5-271:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (904:5-912:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (365:5-365:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (959:5-970:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (413:5-413:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W002::Style/Medium] curly command found (95:5-105:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (480:5-480:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1020:14-1020:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (238:5-238:28)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1021:14-1021:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (644:5-644:28)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1051:6-1051:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (645:5-645:42)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1053:22-1053:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: process_input_ids (276:5-276:36)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1054:16-1054:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_id (105:5-105:22)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1058:16-1058:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_id (270:5-270:22)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1060:13-1060:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_level (143:5-143:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1061:16-1061:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_level (200:5-200:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1076:14-1076:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_level (239:5-239:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1077:14-1077:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_level (273:5-273:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (108:14-108:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_loom (145:5-145:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1102:6-1102:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_name (106:5-106:24)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1104:14-1104:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (510:5-510:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1105:16-1105:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_file_descriptor_objects (577:5-577:52)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1106:16-1106:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_metadata_objects (576:5-576:45)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1108:16-1108:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_type (415:5-415:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1110:13-1110:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_version (417:5-417:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1111:16-1111:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: references (198:5-198:22)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1125:14-1125:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: species (103:5-103:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1149:6-1149:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: species (511:5-511:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1151:21-1151:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ss2_bai_file (147:5-147:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1152:16-1152:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ss2_bam_file (146:5-146:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1153:16-1153:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ss2_index (201:5-201:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1154:16-1154:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: staging_area (737:5-737:24)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1155:13-1155:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: staging_bucket (579:5-579:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1156:17-1156:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: version_timestamp (142:5-142:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1158:17-1158:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: version_timestamp (197:5-197:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1159:16-1159:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: version_timestamp (237:5-237:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1160:13-1160:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: version_timestamp (275:5-275:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1161:17-1161:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: version_timestamp (367:5-367:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1162:17-1162:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: version_timestamp (416:5-416:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1163:16-1163:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/CreateReferenceMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_type (15:5-15:22)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1165:13-1165:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/CreateReferenceMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: pipeline_type (13:5-13:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1166:16-1166:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/CreateReferenceMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_fastas (12:5-12:35)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1190:14-1190:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/CreateReferenceMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: species (16:5-16:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1191:14-1191:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:projects/tasks/CreateReferenceMetadata.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: version_timestamp (14:5-14:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1192:14-1192:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W002::Style/Medium] curly command found (275:3-277:4)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1193:14-1193:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (273:5-273:88)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (139:6-139:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: expressions (108:5-108:30)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (141:14-141:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gnomad_vcf (100:5-100:20)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (142:14-142:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gnomad_vcf_index (101:5-101:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (144:16-144:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: infoFields (209:9-209:33)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (148:16-148:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: interval (102:5-102:20)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (149:13-149:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mem (107:5-107:17)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (150:16-150:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mem (240:9-240:21)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (165:14-165:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: original_vcf (270:5-270:22)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (166:14-166:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: original_vcf_index (271:5-271:28)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (191:6-191:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (105:5-105:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (193:14-193:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (272:5-272:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (194:14-194:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (106:5-106:18)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (195:14-195:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (103:5-103:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (196:14-196:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (104:5-104:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (197:14-197:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tables (239:9-239:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (199:17-199:47)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (161:9-161:17)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (200:17-200:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (185:9-185:17)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (201:17-201:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (98:5-98:13)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (202:17-202:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf_index (162:9-162:23)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (203:17-203:47)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf_index (99:5-99:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (204:17-204:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chr_prefix (10:9-10:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (206:17-206:49)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gnomad_af_expressions (11:9-11:44)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (207:17-207:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gnomad_vcf_prefix (9:9-9:33)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (209:13-209:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: merge_mem (17:9-17:23)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (210:13-210:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_dict (16:9-16:28)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (212:13-212:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_fasta (14:9-14:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (213:16-213:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_index (15:9-15:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (236:15-236:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: thouandG_vcf_index (7:9-7:32)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (237:15-237:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: thousandG_af_expressions (12:9-12:47)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (238:15-238:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: thousandG_vcf (6:9-6:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (239:15-239:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/FilterAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: table (21:3-21:13)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/FilterAFComparisonTable.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: table (6:3-6:13)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (240:15-240:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bad_sites_list (198:9-198:28)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (241:15-241:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: basename (199:9-199:24)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (242:15-242:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: basename (233:5-233:20)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (243:15-243:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: basename (255:5-255:20)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (244:15-244:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_space (234:5-234:46)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (245:15-245:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_space (256:5-256:46)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (246:15-246:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_space (281:5-281:56)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (247:15-247:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: idsList (280:5-280:17)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (248:15-248:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: par1_end (109:9-109:21)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (249:15-249:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: par2_end (111:9-111:21)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (250:15-250:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: par2_start (110:9-110:23)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (251:15-251:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (149:9-149:17)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (252:15-252:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (172:9-172:17)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (253:15-253:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (232:5-232:13)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (255:21-255:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (254:5-254:13)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf_index (150:9-150:23)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bad_sites_list (8:9-8:28)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:16-29:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chrX_vcf (7:9-7:22)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:13-31:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vcfs (6:9-6:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (327:6-327:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_name (26:5-26:21)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (329:14-329:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_recalibrated_bam (24:5-24:31)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:16-32:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_recalibrated_bam_index (25:5-25:37)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (330:14-330:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_file (32:5-32:37)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (331:14-331:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_index (33:5-33:38)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (333:16-333:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database_file (29:5-29:33)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (335:16-335:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: papi_settings (31:5-31:31)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (338:13-338:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: recalibrated_bam_base_name (28:5-28:38)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (339:16-339:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: references (30:5-30:44)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (383:6-383:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_name (27:5-27:23)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (385:14-385:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W002::Style/Medium] curly command found (141:3-152:4)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (386:14-386:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: allow_empty_ref_alt (36:5-36:40)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (387:14-387:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bwa_commandline (24:5-24:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (388:14-388:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (132:5-132:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (389:14-389:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (32:5-32:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (390:14-390:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hard_clip_reads (34:5-34:36)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (391:22-391:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (130:5-130:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (394:16-394:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (23:5-23:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (396:13-396:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: n_reads (131:5-131:16)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (397:16-397:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (25:5-25:31)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (415:14-415:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (133:5-133:30)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (416:14-416:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (33:5-33:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (448:6-448:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_fasta (30:5-30:35)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (451:14-451:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unmap_contaminant_reads (35:5-35:43)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (452:14-452:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W002::Style/Medium] curly command found (150:3-162:4)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (453:14-453:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W002::Style/Medium] curly command found (210:3-228:4)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (456:16-456:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W002::Style/Medium] curly command found (251:3-256:6)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (458:13-458:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W002::Style/Medium] curly command found (287:3-294:6)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (459:16-459:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W002::Style/Medium] curly command found (322:3-329:6)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (46:14-46:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W002::Style/Medium] curly command found (37:3-47:4)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (501:6-501:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W002::Style/Medium] curly command found (95:3-108:4)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (503:14-503:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_disk (191:5-191:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (504:14-504:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_disk (25:5-25:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (505:14-505:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_disk (277:5-277:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (506:14-506:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_disk (78:5-78:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (507:14-507:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bait_set_name (343:5-343:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (508:16-508:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bin_base_qualities (192:5-192:38)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (510:14-510:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bqsr_scatter (135:5-135:21)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (511:14-511:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bqsr_scatter (187:5-187:21)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (512:14-512:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (186:5-186:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (515:16-515:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (24:5-24:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (516:13-516:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (275:5-275:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (517:16-517:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (315:5-315:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (565:6-565:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (70:5-70:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (567:14-567:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_sites_bed (346:5-346:33)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (568:16-568:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_sites_bed (411:5-411:33)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (570:16-570:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_sites_mu (347:5-347:32)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (572:16-572:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_sites_mu (412:5-412:32)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (586:14-586:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_sites_ud (345:5-345:32)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (609:6-609:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_sites_ud (410:5-410:32)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (611:22-611:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_underestimation_factor (417:5-417:47)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (612:22-612:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_vcf (128:5-128:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (613:16-613:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_vcf_index (129:5-129:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (614:17-614:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disable_sanity_check (418:5-418:41)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (616:13-616:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (420:6-420:121)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (617:17-617:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (137:5-137:61)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (618:17-618:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (189:5-189:61)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (620:13-620:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (248:5-248:61)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (621:13-621:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (21:5-21:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (623:13-623:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (408:5-408:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (624:16-624:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (125:5-125:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (642:14-642:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (179:5-179:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (643:14-643:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (409:5-409:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (644:15-644:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bams (272:5-272:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (674:6-674:16)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bams (312:5-312:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (676:22-676:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bams (66:5-66:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (677:22-677:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bqsr_reports (245:5-245:35)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (678:16-678:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: known_indels_sites_indices (131:5-131:43)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (680:13-680:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: known_indels_sites_vcfs (130:5-130:40)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (681:17-681:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (190:5-190:30)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (682:17-682:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (26:5-26:30)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (684:16-684:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (278:5-278:30)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (686:13-686:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (77:5-77:30)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (687:16-687:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_filename (68:5-68:28)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (704:14-704:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (180:5-180:31)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (70:6-70:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (22:5-22:31)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (72:14-72:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (273:5-273:31)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (733:6-733:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (313:5-313:31)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (735:22-735:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (67:5-67:31)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (736:16-736:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_prefix (415:5-415:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (737:16-737:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_report_filename (246:5-246:34)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (738:17-738:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (136:5-136:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (73:14-73:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (188:5-188:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (740:13-740:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (23:5-23:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (741:17-741:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (247:5-247:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (742:17-742:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (276:5-276:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (74:14-74:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (316:5-316:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (752:13-752:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (348:5-348:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (753:16-753:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (416:5-416:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (755:13-755:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (71:5-71:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (756:16-756:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_name_regex (76:5-76:28)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (75:14-75:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: recalibration_report (181:5-181:30)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (76:14-76:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: recalibration_report_filename (126:5-126:41)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (784:14-784:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (132:5-132:18)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (785:14-785:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (183:5-183:18)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (786:15-786:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (133:5-133:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (787:14-787:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (184:5-184:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (820:6-820:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (413:5-413:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (822:22-822:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (134:5-134:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (823:22-823:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (185:5-185:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (824:16-824:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (414:5-414:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (825:13-825:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sequence_group_interval (127:5-127:42)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (826:17-826:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sequence_group_interval (182:5-182:42)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (834:17-834:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: somatic (193:5-193:28)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (836:16-836:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sorting_collection_size_ratio (80:5-80:41)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (838:13-838:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: target_interval_list (344:5-344:30)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (839:16-839:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: total_input_size (274:5-274:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (84:14-84:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: total_input_size (314:5-314:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (857:14-857:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: total_input_size (69:5-69:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (858:14-858:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamToCram.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: agg_preemptible_tries (16:5-16:30)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (85:14-85:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamToCram.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (15:5-15:26)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (87:13-87:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamToCram.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chimerism_metrics (14:5-14:27)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (886:6-886:16)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamToCram.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplication_metrics (13:5-13:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (888:14-888:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamToCram.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (9:5-9:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (889:14-889:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamToCram.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (12:5-12:18)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (88:13-88:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamToCram.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (10:5-10:19)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (892:16-892:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/BamToCram.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (11:5-11:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (894:13-894:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_disk (19:9-19:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (895:16-895:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_vcf (13:9-13:31)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (897:15-897:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_vcf_index (14:9-14:37)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (900:12-900:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (17:9-17:65)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (901:12-901:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_override (18:9-18:28)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (902:12-902:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: intervals (5:9-5:24)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (915:14-915:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (22:9-22:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (916:15-916:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (20:9-20:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (917:15-917:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: normal_crai_or_bai (12:9-12:33)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (91:13-91:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: normal_cram_or_bam (11:9-11:33)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (92:16-92:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_attempts (21:9-21:34)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (949:6-949:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference (6:9-6:23)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (954:16-954:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_dict (7:9-7:28)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (956:16-956:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_index (8:9-8:29)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (983:6-983:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tumor_crai_or_bai (10:9-10:31)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (985:14-985:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CheckContaminationSomatic.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tumor_cram_or_bam (9:9-9:31)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (986:16-986:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" -message = "[v1::W002::Style/Medium] curly command found (28:3-59:4)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (987:17-987:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: base_file_name (25:5-25:40)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (988:17-988:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination (24:5-24:25)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (989:13-989:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: destination_cloud_path (21:5-21:34)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (990:13-990:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: files_to_copy (20:5-20:32)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (991:17-991:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: google_account_vault_path (23:5-23:37)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (992:17-992:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/CopyFilesFromCloudToCloud.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vault_token_path (22:5-22:28)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (997:13-997:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (46:1-46:2)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (998:13-998:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W001::Style/Low] trailing space (36:46)" +document = "biowdl/tasks:picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (999:16-999:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W001::Style/Low] trailing space (42:123)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (58:1-58:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W001::Style/Low] trailing space (5:87)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W001::Style/Low] trailing space (84:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W001::Style/Low] trailing space (6:54)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W002::Style/Medium] curly command found (33:5-39:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: alignment (25:5-25:19)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W002::Style/Medium] curly command found (75:5-82:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: alignment_index (26:5-26:25)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: dgeAnnotation (104:9-104:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (27:5-27:56)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: dgeDesign (60:9-60:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (30:5-30:19)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (28:5-28:30)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (23:5-23:18)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:16-26:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (21:5-21:19)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:13-29:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_idx (22:5-22:23)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:16-30:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: str_table_file (24:5-24:24)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (42:14-42:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: threads (29:5-29:20)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (64:6-64:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragenTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_ssd (31:5-31:27)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (66:14-66:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (29:5-29:26)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (67:14-67:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (35:5-35:17)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (68:16-68:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_multiplier (36:5-36:30)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (71:13-71:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (34:5-34:92)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (72:16-72:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dragmap_reference (27:5-27:39)" +document = "biowdl/tasks:prepareShiny.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (85:14-85:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hard_clip_reads (31:5-31:36)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W002::Style/Medium] curly command found (35:5-41:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (23:5-23:19)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: allStats (181:9-181:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (37:5-37:26)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: falseNegativesVcf (169:9-169:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (24:5-24:31)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: falseNegativesVcfIndex (170:9-170:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (30:5-30:26)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: falsePositivesVcf (171:9-171:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_fasta (26:5-26:35)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: falsePositivesVcfIndex (172:9-172:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/DragmapAlignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unmap_contaminant_reads (32:5-32:43)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: nonSnpRoc (178:9-178:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (112:3-131:4)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: phasing (179:9-179:16)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (158:3-164:4)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: sdf (64:9-64:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (189:3-197:4)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: summary (173:9-173:16)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (224:3-226:4)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: truePositivesBaselineVcf (174:9-174:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (250:3-271:4)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: truePositivesBaselineVcfIndex (175:9-175:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (352:3-357:4)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: truePositivesVcf (176:9-176:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (526:3-536:4)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: truePositivesVcfIndex (177:9-177:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (65:3-71:4)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: weightedRoc (180:9-180:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: analysis_version_number (95:5-95:32)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (113:14-113:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bead_pool_manifest_csv_file (33:5-33:37)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (114:14-114:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bead_pool_manifest_csv_file (61:5-61:39)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (115:14-115:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bead_pool_manifest_file (463:5-463:33)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (116:14-116:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bead_pool_manifest_file (59:5-59:33)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (118:14-118:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bead_pool_manifest_file (93:5-93:33)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:14-119:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: call_intervals_file (592:5-592:29)" 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call_vcf_file (590:5-590:23)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (124:14-124:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: call_vcf_index_file (591:5-591:29)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (125:21-125:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chain_file (704:5-704:20)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcode (460:5-460:29)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:22-25:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_file (464:5-464:23)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_file (60:5-60:22)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:16-29:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_file (691:5-691:22)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:13-31:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_file (92:5-92:22)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:16-32:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_controls_vcf (180:5-180:37)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (68:6-68:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbSNP_vcf_file (288:5-288:24)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (71:14-71:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbSNP_vcf_file (697:5-697:24)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (73:14-73:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbSNP_vcf_index_file (289:5-289:30)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (74:17-74:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbSNP_vcf_index_file (698:5-698:30)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (75:16-75:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (105:5-105:18)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (76:16-76:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (154:5-154:18)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (78:17-78:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (185:5-185:18)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (80:17-80:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (220:5-220:18)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (82:15-82:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (246:5-246:18)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (83:15-83:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (293:5-293:18)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (86:16-86:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (348:5-348:18)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (89:13-89:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (35:5-35:18)" +document = "biowdl/tasks:rtg.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (90:16-90:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (430:5-430:18)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W001::Style/Low] trailing space (94:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (466:5-466:18)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W002::Style/Medium] curly command found (159:5-171:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (522:5-522:18)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W002::Style/Medium] curly command found (35:5-40:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (601:5-601:18)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W002::Style/Medium] curly command found (93:5-107:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (62:5-62:18)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (110:14-110:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (667:5-667:18)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (111:14-111:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (706:5-706:18)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (142:6-142:10)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: excludeFiltered (377:5-377:36)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (144:14-144:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: excludeNonVariants (378:5-378:39)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (145:16-145:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: expected_first_sample_name (242:5-242:38)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (146:17-146:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: extended_chip_manifest_file (91:5-91:37)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (147:13-147:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: 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"[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_threshold (599:5-599:46)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (153:16-153:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: green_idat_cloud_path (461:5-461:31)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (157:12-157:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_adpc_file (215:5-215:25)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (174:14-174:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_cloud_path (5:5-5:26)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (175:14-175:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_csv (689:5-689:19)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:14)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (241:5-241:20)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_gtc (32:5-32:19)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_gtc (89:5-89:19)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf (149:5-149:19)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:13-31:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf (179:5-179:19)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:16-32:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf (214:5-214:19)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (66:6-66:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf (513:5-513:19)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (68:21-68:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_file (286:5-286:24)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (69:16-69:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_file (373:5-373:24)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (70:13-70:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_file (422:5-422:24)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (72:13-72:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_file (555:5-555:24)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (73:13-73:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_file (660:5-660:24)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (74:17-74:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index (150:5-150:25)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (76:14-76:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index (514:5-514:25)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (77:14-77:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index_file (287:5-287:30)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (85:13-85:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index_file (374:5-374:30)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (87:13-87:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index_file (423:5-423:30)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (88:16-88:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index_file (556:5-556:30)" +document = "biowdl/tasks:sambamba.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (91:12-91:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index_file (661:5-661:30)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W002::Style/Medium] curly command found (125:5-131:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: interval_list_filename (346:5-346:34)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W002::Style/Medium] curly command found (174:5-189:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: intervals (554:5-554:19)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W002::Style/Medium] curly command found (240:5-247:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: is_gender_autocall (465:5-465:39)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W002::Style/Medium] curly command found (284:5-288:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: maf_file (151:5-151:19)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W002::Style/Medium] curly command found (328:5-339:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: map_file (516:5-516:18)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W002::Style/Medium] curly command found (36:5-41:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (104:5-104:91)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W002::Style/Medium] curly command found (375:5-379:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: num_markers (217:5-217:20)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W002::Style/Medium] curly command found (417:5-425:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: num_markers_filename (182:5-182:32)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W002::Style/Medium] curly command found (472:5-485:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: num_samples (216:5-216:20)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W002::Style/Medium] curly command found (529:5-537:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_adpc_filename (183:5-183:32)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W002::Style/Medium] curly command found (586:5-601:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (690:5-690:28)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (116:6-116:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_filename (218:5-218:27)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (118:14-118:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_metrics_basefilename (244:5-244:39)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:16-119:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_metrics_basename (291:5-291:35)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (122:16-122:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_metrics_basename (598:5-598:35)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (134:14-134:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_results_filename (152:5-152:35)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (154:6-154:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf_filename (375:5-375:31)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (156:14-156:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf_filename (424:5-424:31)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (157:16-157:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf_filename (520:5-520:31)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (158:17-158:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ped_file (515:5-515:18)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (159:17-159:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (97:5-97:28)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (160:17-160:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (106:5-106:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (161:17-161:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (155:5-155:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (163:14-163:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (186:5-186:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (164:14-164:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (221:5-221:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (165:14-165:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (247:5-247:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (166:14-166:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (294:5-294:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (170:13-170:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (349:5-349:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (171:16-171:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (36:5-36:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (192:14-192:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (385:5-385:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (193:15-193:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (431:5-431:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (194:15-194:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (467:5-467:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (228:6-228:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (523:5-523:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (230:14-230:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (602:5-602:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (231:16-231:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (63:5-63:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (234:13-234:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (668:5-668:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (235:16-235:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (707:5-707:26)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (238:12-238:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: red_idat_cloud_path (462:5-462:29)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (101:5-101:18)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (250:14-250:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (383:5-383:18)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (251:14-251:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (428:5-428:18)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (559:5-559:18)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:16-26:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (665:5-665:18)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (274:6-274:14)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (695:5-695:18)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (276:14-276:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (381:5-381:19)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (277:16-277:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (426:5-426:19)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (280:13-280:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (557:5-557:19)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (281:16-281:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (663:5-663:19)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:13-30:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (693:5-693:19)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (313:6-313:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (99:5-99:19)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (315:14-315:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (100:5-100:25)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (317:17-317:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (382:5-382:25)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:16-31:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (427:5-427:25)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (320:13-320:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (558:5-558:25)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (321:16-321:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (664:5-664:25)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (325:12-325:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (694:5-694:25)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (326:12-326:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reported_gender (96:5-96:27)" +document = 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"[v1::W003::Completeness/Medium] missing parameter meta within task: supported_ref_fasta_index (701:5-701:35)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (372:16-372:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_intervals_file (596:5-596:31)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (382:14-382:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_sample_name (597:5-597:30)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (402:6-402:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_vcf_file (594:5-594:25)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (404:22-404:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_vcf_index_file (595:5-595:31)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (405:16-405:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: variant_rsids_file (379:5-379:29)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case 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identifier must be snake case (428:14-428:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: zcall_ped_filename (30:5-30:30)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (429:14-429:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: zcall_thresholds_file (34:5-34:31)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (455:6-455:10)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: zcall_thresholds_file (517:5-517:31)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (457:14-457:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/IlluminaGenotypingArrayTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: zcall_version (518:5-518:25)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (458:16-458:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (14:3-16:4)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (459:17-459:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (382:3-385:4)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (460:13-460:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (409:3-414:4)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (462:13-462:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (667:3-674:4)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (464:13-464:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (73:3-85:4)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (465:13-465:24)" [[concerns]] kind = "LintWarning" -document = 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"broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: basename (615:5-615:20)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (489:14-489:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: basename (61:5-61:20)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (517:6-517:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: basename (755:5-755:20)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (519:14-519:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: basename (793:5-793:20)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (520:16-520:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: basename (821:5-821:20)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (523:13-523:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bcftools_docker (151:5-151:107)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (524:16-524:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bcftools_docker (307:5-307:107)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (540:14-540:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bcftools_docker (405:5-405:107)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (564:6-564:10)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bcftools_docker (468:5-468:107)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (566:14-566:20)" [[concerns]] kind = "LintWarning" 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"broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (10:5-10:16)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (605:14-605:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (116:5-116:16)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (69:6-69:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (152:5-152:16)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (71:14-71:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (192:5-192:16)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (72:16-72:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (229:5-229:16)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (74:13-74:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (270:5-270:16)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (75:16-75:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (340:5-340:16)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (78:12-78:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (35:5-35:16)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (80:12-80:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (376:5-376:16)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (90:14-90:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (406:5-406:16)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (91:14-91:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (436:5-436:16)" +document = "biowdl/tasks:samtools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (92:14-92:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (470:5-470:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W002::Style/Medium] curly command found (35:5-46:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (508:5-508:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fractionOrNumber (28:9-28:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (533:5-533:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outFilePath (26:9-26:53)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (581:5-581:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preCommand (31:9-31:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (618:5-618:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: seed (32:9-32:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (660:5-660:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sequenceFile (25:9-25:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (66:5-66:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: twoPassMode (27:9-27:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (706:5-706:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: zip (29:9-29:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (734:5-734:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W005::Completeness/Medium] missing runtime block within a task (23:1-51:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (758:5-758:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (796:5-796:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (824:5-824:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:16-26:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (855:5-855:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:17-27:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (879:5-879:16)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:15-28:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dataset_bcf (182:5-182:21)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:17-31:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dataset_bcf_index (183:5-183:27)" +document = "biowdl/tasks:seqtk.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (49:14-49:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (118:5-118:96)" +document = "biowdl/tasks:smoove.wdl" +message = "[v1::W002::Style/Medium] curly command found (37:5-47:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (11:5-11:57)" +document = "biowdl/tasks:smoove.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: smooveVcf (72:9-72:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (150:5-150:89)" +document = "biowdl/tasks:smoove.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:10)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (194:5-194:132)" +document = "biowdl/tasks:smoove.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (231:5-231:85)" +document = "biowdl/tasks:smoove.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (272:5-272:55)" +document = "biowdl/tasks:smoove.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:14-27:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (338:5-338:80)" +document = "biowdl/tasks:smoove.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:14-28:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (36:5-36:57)" +document = "biowdl/tasks:smoove.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:16-30:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (374:5-374:93)" +document = "biowdl/tasks:smoove.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:13-33:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (404:5-404:94)" +document = "biowdl/tasks:smoove.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:16-34:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (438:5-438:87)" +document = "biowdl/tasks:smoove.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:14-50:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (471:5-471:95)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W002::Style/Medium] curly command found (45:5-63:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (510:5-510:52)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:6-25:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (535:5-535:57)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:14-28:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (583:5-583:26)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:16-29:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (620:5-620:56)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:14-30:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (659:5-659:53)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:16-31:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (65:5-65:53)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:17-34:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (708:5-708:58)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:17-35:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (732:5-732:54)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:17-36:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (760:5-760:56)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:14-37:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (798:5-798:56)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (40:16-40:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (826:5-826:57)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:13-41:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (857:5-857:77)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (42:16-42:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (883:5-883:89)" +document = "biowdl/tasks:snpeff.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (66:14-66:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: eagle_docker (191:5-191:92)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W002::Style/Medium] curly command found (171:5-196:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: end (189:5-189:12)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W002::Style/Medium] curly command found (279:5-296:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: end (225:5-225:12)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W002::Style/Medium] curly command found (371:5-389:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: end (59:5-59:12)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W002::Style/Medium] curly command found (449:5-456:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: end (656:5-656:12)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W002::Style/Medium] curly command found (56:5-80:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ends (574:5-574:20)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: consensusIndels (245:9-245:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: exclude_filtered (657:5-657:37)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: consensusIndels (430:9-430:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file1 (851:5-851:15)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: consensusSNV (246:9-246:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file2 (852:5-852:15)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: consensusSNV (431:9-431:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (115:5-115:61)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleIndels (133:9-133:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (269:5-269:61)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleIndels (247:9-247:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (339:5-339:61)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleIndels (341:9-341:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (375:5-375:61)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleIndels (432:9-432:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (662:5-662:61)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleIndelsClassifier (249:9-249:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (68:5-68:61)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleIndelsClassifier (434:9-434:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (757:5-757:61)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleSNV (134:9-134:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (823:5-823:61)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleSNV (248:9-248:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genetic_map_file (187:5-187:26)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleSNV (342:9-342:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ids (754:5-754:13)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleSNV (433:9-433:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: included_contigs (31:5-31:26)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleSNVClassifier (250:9-250:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: infoFile (528:5-528:18)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: ensembleSNVClassifier (435:9-435:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf (429:5-429:19)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: indels (131:9-131:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index (430:5-430:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: indels (339:9-339:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_indices (465:5-465:34)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputVcf (477:9-477:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcfs (266:5-266:27)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: snvs (132:9-132:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcfs (464:5-464:27)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: snvs (340:9-340:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (117:5-117:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (138:6-138:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (153:5-153:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (140:14-140:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (193:5-193:26)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (141:14-141:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (230:5-230:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (142:16-142:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (271:5-271:26)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (143:14-143:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (341:5-341:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (144:14-144:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (34:5-34:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (145:14-145:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (377:5-377:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (146:14-146:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (407:5-407:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (147:14-147:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (437:5-437:26)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (148:14-148:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (469:5-469:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (150:15-150:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (509:5-509:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (151:15-151:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (534:5-534:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (152:15-152:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (582:5-582:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (153:15-153:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (619:5-619:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (154:15-154:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (661:5-661:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (155:15-155:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (67:5-67:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (156:15-156:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (707:5-707:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (157:15-157:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (735:5-735:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (158:15-158:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (759:5-759:26)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (159:15-159:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (797:5-797:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (160:15-160:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (825:5-825:26)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (161:15-161:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (856:5-856:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (162:15-162:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (880:5-880:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (163:15-163:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (9:5-9:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (167:13-167:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics (614:5-614:24)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (168:16-168:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimac4_docker (228:5-228:100)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (199:14-199:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: multiSampleVcf (875:5-875:24)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (200:14-200:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nSamples (529:5-529:17)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (201:14-201:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nSamples (876:5-876:17)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (202:14-202:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: optional_qc_hwe (433:5-433:27)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (203:14-203:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: optional_qc_max_missing (432:5-432:35)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (204:14-204:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: original_vcf (370:5-370:22)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: original_vcf (400:5-400:22)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (254:6-254:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: original_vcf_index (371:5-371:28)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (257:14-257:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: original_vcf_index (401:5-401:28)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (258:16-258:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (372:5-372:27)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (259:14-259:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (402:5-402:27)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:16-25:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (653:5-653:27)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (260:14-260:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (703:5-703:27)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (262:15-262:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (730:5-730:27)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (263:15-263:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf_basename (267:5-267:31)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (264:15-264:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf_basename (431:5-431:31)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (265:15-265:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf_basename (466:5-466:31)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (266:15-266:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: panel_vcf (112:5-112:19)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (267:15-267:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: panel_vcf (145:5-145:19)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (268:15-268:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: panel_vcf_index (113:5-113:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (269:15-269:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: panel_vcf_index (146:5-146:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: phased_vcf (221:5-221:20)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (270:15-270:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (222:5-222:18)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (271:15-271:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (30:5-30:18)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (275:13-275:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (335:5-335:18)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (276:16-276:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (5:5-5:18)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:14-27:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_panel (220:5-220:19)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:14-28:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_panel_bcf (184:5-184:29)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:14-29:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_panel_bcf_index (185:5-185:35)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (305:14-305:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rtidyverse_docker (532:5-532:56)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (306:14-306:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rtidyverse_docker (580:5-580:56)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:14-30:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rtidyverse_docker (617:5-617:56)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:14-31:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: start (188:5-188:14)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:15-33:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: start (224:5-224:14)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (346:6-346:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: start (58:5-58:14)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (349:14-349:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: start (655:5-655:14)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:15-34:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: starts (573:5-573:22)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (350:14-350:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ubuntu_docker (33:5-33:42)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (351:14-351:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ubuntu_docker (854:5-854:42)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (352:16-352:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ubuntu_docker (8:5-8:42)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (353:14-353:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valids (577:5-577:26)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (354:14-354:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: var_in_original (147:5-147:24)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (356:15-356:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: var_in_reference (148:5-148:25)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (357:15-357:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vars_in_array (575:5-575:29)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (358:15-358:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vars_in_panel (576:5-576:29)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (359:15-359:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (110:5-110:13)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:15-35:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (143:5-143:13)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (360:15-360:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (333:5-333:13)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (361:15-361:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (505:5-505:13)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (362:15-362:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (702:5-702:13)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (363:15-363:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (729:5-729:13)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (367:13-367:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (792:5-792:13)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (368:16-368:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf_index (111:5-111:19)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:15-36:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf_index (144:5-144:19)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:15-37:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf_index (334:5-334:19)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:15-38:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf_to_replace_header (304:5-304:31)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (392:14-392:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf_with_new_header (305:5-305:29)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (393:14-393:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcfs (820:5-820:21)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (394:14-394:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: window (226:5-226:15)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (395:14-395:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (148:3-153:4)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (396:14-396:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: analysis_version_number (12:5-12:32)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (397:14-397:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: analysis_version_number (44:5-44:32)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (39:15-39:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: analysis_version_number_output (497:9-497:47)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (40:15-40:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: arrays_chip_metadata_path (430:5-430:37)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:15-41:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: arrays_chip_metadata_path (462:5-462:37)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (42:15-42:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: arrays_control_code_summary_metrics (170:5-170:45)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (439:6-439:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: arrays_variant_calling_control_metrics_file (506:9-506:60)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (43:15-43:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: arrays_variant_calling_detail_metrics (168:5-168:47)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (441:14-441:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: arrays_variant_calling_detail_metrics (245:5-245:47)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (442:16-442:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: arrays_variant_calling_detail_metrics_file (504:9-504:59)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (445:13-445:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: arrays_variant_calling_summary_metrics (169:5-169:48)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (446:16-446:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: arrays_variant_calling_summary_metrics_file (505:9-505:60)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (44:15-44:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: authentication (180:5-180:33)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (459:14-459:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: authentication (248:5-248:33)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (45:15-45:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: authentication (354:5-354:33)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (46:15-46:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: authentication (392:5-392:33)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (47:15-47:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: authentication (47:5-47:33)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (48:15-48:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: autocall_version (9:5-9:28)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (52:13-52:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: baf_regress_metrics_file (498:9-498:41)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (53:16-53:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bafregress_metrics (177:5-177:29)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (89:14-89:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bpm_filename (428:5-428:24)" +document = "biowdl/tasks:somaticseq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (90:14-90:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bpm_filename (461:5-461:24)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W002::Style/Medium] curly command found (57:5-87:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_type (7:5-7:21)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: careful (44:9-44:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_type_name (294:5-294:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: covCutoff (50:9-50:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcode (295:5-295:29)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dataset (47:9-47:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcode (389:5-389:29)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disableGzipOutput (45:9-45:42)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcode (43:5-43:29)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disableRepeatResolution (46:9-46:48)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcode (5:5-5:29)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: interlacedReads (30:9-30:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcode_output (496:9-496:41)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ionTorrent (41:9-41:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_filename (11:5-11:28)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: k (49:9-49:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: collaborator_participant_id (296:5-296:40)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memoryGb (54:9-54:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (144:5-144:18)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metagenomic (38:9-38:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (183:5-183:18)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nanoporeReads (33:9-33:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (251:5-251:18)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: onlyAssembler (43:9-43:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (356:5-356:18)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: onlyErrorCorrection (42:9-42:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (89:5-89:18)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputDir (27:9-27:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: egt_filename (429:5-429:24)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pacbioReads (32:9-32:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: extended_manifest_map_file (427:5-427:36)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: phredOffset (51:9-51:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fingerprint_detail_metrics_file (508:9-508:48)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: plasmid (40:9-40:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fingerprint_summary_metrics_file (509:9-509:49)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preCommand (29:9-29:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fingerprinting_detail_metrics (171:5-171:40)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read1 (25:9-25:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fingerprinting_summary_metrics (172:5-172:41)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read2 (26:9-26:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gender (307:5-307:18)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rna (39:9-39:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_contingency_metrics (175:5-175:51)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sangerReads (31:9-31:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_contingency_metrics_file (513:9-513:62)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: singleCell (37:9-37:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_detail_metrics (174:5-174:46)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: threads (53:9-53:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_detail_metrics_file (512:9-512:57)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tmpDir (48:9-48:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_summary_metrics (173:5-173:47)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: trustedContigs (35:9-35:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_summary_metrics_file (511:9-511:58)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tslrContigs (34:9-34:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gtc_file (499:9-499:25)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: untrustedContigs (36:9-36:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (141:5-141:20)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_file (84:5-84:24)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index_file (85:5-85:30)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:15-26:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lab_batch (297:5-297:22)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lab_batch (515:9-515:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:17-29:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minor_allele_frequency_map_file (460:5-460:41)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:15-30:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: notes (50:5-50:17)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:15-31:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_json_filename (88:5-88:32)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:15-32:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_metrics_basefilename (142:5-142:39)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:15-33:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_metrics_basename (10:5-10:35)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:15-34:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf (501:9-501:27)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:15-35:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf_index (502:9-502:33)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:15-36:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: params_file (352:5-352:21)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:17-37:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: participant_id (298:5-298:27)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:17-41:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (13:5-13:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (42:17-42:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (145:5-145:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (43:17-43:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (184:5-184:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (45:17-45:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (252:5-252:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (46:17-46:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (310:5-310:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (48:15-48:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (357:5-357:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:16-50:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (390:5-390:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (51:14-51:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (431:5-431:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (54:13-54:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (45:5-45:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (90:21-90:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (463:5-463:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (93:14-93:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (90:5-90:26)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (94:14-94:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: product_family (299:5-299:27)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (95:14-95:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: product_name (300:5-300:25)" +document = "biowdl/tasks:spades.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (96:14-96:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: product_order_id (301:5-301:29)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W001::Style/Low] trailing space (137:87)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: product_part_number (302:5-302:32)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W002::Style/Medium] curly command found (146:5-166:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: product_type (303:5-303:24)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W002::Style/Medium] curly command found (217:5-219:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reason (49:5-49:18)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W002::Style/Medium] curly command found (37:5-47:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: regulatory_designation (304:5-304:34)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: bamFile (204:9-204:16)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reported_gender (8:5-8:27)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: chrLength (91:9-91:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: research_project_id (305:5-305:31)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: chrName (93:9-93:16)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_alias (306:5-306:24)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: chrNameLength (92:9-92:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_alias (6:5-6:24)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: chrStart (94:9-94:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_id (308:5-308:22)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: exonGeTrInfo (99:9-99:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_lsid (309:5-309:23)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: exonInfo (100:9-100:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_lsid (87:5-87:23)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: geneInfo (101:9-101:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: service_account_filename (181:5-181:36)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: genome (95:9-95:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: service_account_filename (249:5-249:36)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: genomeParameters (96:9-96:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: service_account_filename (355:5-355:36)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: logFinalOut (205:9-205:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: service_account_filename (393:5-393:36)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: sa (97:9-97:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: service_account_filename (48:5-48:36)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: saIndex (98:9-98:16)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: upload_metrics_output (42:5-42:31)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: sjdbInfo (102:9-102:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: variant_calling_detail_metrics_file (86:5-86:45)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: sjdbListFromGtfOut (103:9-103:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vault_token_path (179:5-179:26)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: sjdbListOut (104:9-104:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vault_token_path (247:5-247:26)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: starIndex (106:9-106:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vault_token_path (353:5-353:26)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: transcriptInfo (105:9-105:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vault_token_path (391:5-391:26)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: library (212:9-212:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vault_token_path (46:5-46:26)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: platform (213:9-213:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: verify_id_metrics (176:5-176:28)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: readgroup (214:9-214:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (140:1-140:8)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample (211:9-211:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: aggregated_imputation_metrics (5:9-5:54)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W005::Completeness/Medium] missing runtime block within a task (209:1-224:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcodes (12:9-12:43)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (110:6-110:10)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chunks_info (6:9-6:36)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (112:22-112:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: failed_chunks (7:9-7:38)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (113:21-113:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: imputation_outputs_tsv (130:9-130:47)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (114:22-114:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: imputed_multisample_vcf (8:9-8:48)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (115:16-115:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: imputed_multisample_vcf_index (9:9-9:54)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (116:16-116:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: imputed_single_sample_vcf_indices (11:9-11:58)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (117:16-117:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: imputed_single_sample_vcf_indices (63:9-63:58)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (118:13-118:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: imputed_single_sample_vcfs (10:9-10:51)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (120:14-120:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: imputed_single_sample_vcfs (62:9-62:51)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (121:16-121:42)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lab_batches (133:9-133:36)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (122:14-122:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: n_failed_chunks (13:9-13:40)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (123:16-123:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_task (129:9-129:33)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (124:17-124:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: timestamp (132:9-132:34)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (125:17-125:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: trigger_bucket_path (131:9-131:44)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (126:24-126:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (1085:3-1092:4)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (127:17-127:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (1123:3-1129:4)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (128:14-128:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (13:3-27:4)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (130:13-130:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (968:3-979:4)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (133:13-133:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_annotation (156:5-156:34)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (134:16-134:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: allow_old_rms_mapping_quality_annotation_data (161:5-161:66)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (138:9-138:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotations_to_divide (1111:5-1111:92)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (144:25-144:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: axiomPoly_resource_vcf (328:5-328:32)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (169:14-169:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: axiomPoly_resource_vcf_index (331:5-331:38)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (170:14-170:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: base_output_name (702:5-702:28)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (209:6-209:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: batch_size (95:5-95:19)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (222:16-222:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_resource_vcf (329:5-329:28)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_resource_vcf (393:5-393:28)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:16-25:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_resource_vcf (458:5-458:28)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_resource_vcf_index (332:5-332:34)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:15-28:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_resource_vcf_index (397:5-397:34)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:14-29:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_resource_vcf_index (462:5-462:34)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:13-33:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_vcf (153:5-153:21)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:16-34:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_vcf (216:5-216:21)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:14-50:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_vcf (752:5-752:19)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (51:14-51:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_vcf_index (753:5-753:25)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (52:14-52:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (880:5-880:19)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (53:14-53:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (1000:5-1000:26)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (55:14-55:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (1080:5-1080:26)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (57:14-57:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (10:5-10:26)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (58:15-58:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (1114:5-1114:50)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (59:15-59:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (158:5-158:21)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (60:15-60:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (221:5-221:110)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (61:15-61:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (277:5-277:21)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (62:15-62:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (336:5-336:21)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (63:15-63:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (401:5-401:21)" +document = "biowdl/tasks:star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (64:15-64:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (466:5-466:21)" +document = 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"[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (756:5-756:21)" +document = "biowdl/tasks:strelka.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: variants (88:9-88:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (795:5-795:21)" +document = "biowdl/tasks:strelka.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: variantsIndex (170:9-170:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (93:5-93:21)" +document = "biowdl/tasks:strelka.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: variantsIndex (89:9-89:22)" [[concerns]] kind = 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(101:14-101:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: excess_het_threshold (272:5-272:31)" +document = "biowdl/tasks:strelka.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (104:15-104:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: expected_inconclusive_samples (877:5-877:53)" +document = "biowdl/tasks:strelka.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (105:15-105:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: extra_args (53:5-53:23)" +document = "biowdl/tasks:strelka.wdl" +message = "[v1::W006::Naming/Low] 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identifier must be snake case (58:14-58:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (704:5-704:30)" +document = "biowdl/tasks:stringtie.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (59:15-59:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (757:5-757:30)" +document = "biowdl/tasks:stringtie.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (91:6-91:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (796:5-796:30)" +document = "biowdl/tasks:stringtie.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (93:22-93:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (879:5-879:24)" +document = "biowdl/tasks:stringtie.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (94:16-94:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (94:5-94:31)" +document = "biowdl/tasks:stringtie.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (95:17-95:57)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (965:5-965:30)" +document = "biowdl/tasks:stringtie.wdl" 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(1117:5-1117:24)" +document = "biowdl/tasks:survivor.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:21-25:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (1115:5-1115:26)" +document = "biowdl/tasks:survivor.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:13-26:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_filename_prefix (751:5-751:35)" +document = "biowdl/tasks:survivor.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:13-27:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: 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parameter meta within task: mode (529:5-529:16)" +document = "biowdl/tasks:survivor.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:13-31:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: model_report (447:5-447:23)" +document = "biowdl/tasks:survivor.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:16-32:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: model_report_filename (382:5-382:33)" +document = "biowdl/tasks:survivor.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:13-35:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: omni_resource_vcf (391:5-391:27)" +document = "biowdl/tasks:survivor.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:16-36:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: omni_resource_vcf (456:5-456:27)" +document = "biowdl/tasks:survivor.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (55:14-55:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: omni_resource_vcf_index (395:5-395:33)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W002::Style/Medium] curly command found (152:5-164:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: omni_resource_vcf_index (460:5-460:33)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W002::Style/Medium] curly command found (208:5-216:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: one_thousand_genomes_resource_vcf (392:5-392:43)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W002::Style/Medium] curly command found (258:5-266:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: one_thousand_genomes_resource_vcf (457:5-457:43)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W002::Style/Medium] curly command found (310:5-322:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: one_thousand_genomes_resource_vcf_index (396:5-396:49)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W002::Style/Medium] curly command found (368:5-379:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: one_thousand_genomes_resource_vcf_index (461:5-461:49)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W002::Style/Medium] curly command found (38:5-48:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_base_name (875:5-875:28)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W002::Style/Medium] curly command found (421:5-425:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_file_name (963:5-963:28)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W002::Style/Medium] curly command found (462:5-470:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_filename (528:5-528:27)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W002::Style/Medium] curly command found (94:5-105:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_prefix (794:5-794:25)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: abundanceFile (73:9-73:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf_filename (147:5-147:31)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: databaseFile (349:9-349:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf_filename (212:5-212:31)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: gtfFile (131:9-131:16)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf_name (654:5-654:27)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: labeledSam (407:9-407:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (1116:5-1116:24)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: readAnnotations (239:9-239:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: recalibrated_vcf_filename (592:5-592:37)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: readLabels (408:9-408:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing 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[[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: recalibration_filename (318:5-318:34)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: talonAnnotation (568:9-568:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: recalibration_filename (379:5-379:34)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: talonConfigFile (569:9-569:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: recalibration_filename (445:5-445:34)" +document = 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"broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: recalibration_tranche_values (449:5-449:47)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (108:14-108:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (151:5-151:18)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (135:6-135:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (215:5-215:18)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (137:14-137:26)" [[concerns]] kind = "LintWarning" 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"broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (149:5-149:19)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (141:13-141:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (213:5-213:19)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (142:17-142:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (46:5-46:19)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (144:15-144:27)" [[concerns]] kind = "LintWarning" -document = 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"LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: calling_interval_list_index (620:5-620:38)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (459:16-459:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chimerism_metrics (356:5-356:27)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (473:14-473:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: collect_gc_bias_metrics (101:5-101:43)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (497:6-497:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: collect_gc_bias_metrics (149:5-149:43)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (499:21-499:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cross_check_by (252:5-252:26)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (501:16-501:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_vcf (617:5-617:20)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (502:14-502:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_vcf (671:5-671:19)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (503:16-503:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_vcf_index (618:5-618:26)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (504:15-504:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbsnp_vcf_index (672:5-672:25)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (505:15-505:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (417:5-420:63)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (506:16-506:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplication_metrics (355:5-355:29)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (510:13-510:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: evaluation_interval_list (674:5-674:34)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (511:16-511:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: expected_sample_alias (290:5-290:33)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (51:14-51:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: extra_args (623:5-623:23)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (537:14-537:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (624:5-624:61)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (538:14-538:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_lod_threshold (293:5-293:39)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (539:14-539:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotypes (288:5-288:19)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (540:14-540:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotypes_index (289:5-289:26)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (78:6-78:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: haplotype_database_file (247:5-247:33)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (80:14-80:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: haplotype_database_file (295:5-295:33)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (81:16-81:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ignore (411:5-411:26)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (82:16-82:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (143:5-143:19)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (83:16-83:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (21:5-21:19)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (84:17-84:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (282:5-282:20)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (86:15-86:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (404:5-404:19)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (87:15-87:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (452:5-452:19)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (90:13-90:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (491:5-491:19)" +document = "biowdl/tasks:talon.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (91:16-91:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (50:5-50:19)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (193:1-193:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (533:5-533:19)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W002::Style/Medium] curly command found (136:5-156:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (584:5-584:19)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W002::Style/Medium] curly command found (35:5-43:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (95:5-95:19)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W002::Style/Medium] curly command found (80:5-86:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (144:5-144:25)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: fastaFile (195:9-195:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (283:5-283:26)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: logFile (196:9-196:16)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (405:5-405:26)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: logFileTE (198:9-198:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (453:5-453:25)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputSam (197:9-197:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (492:5-492:25)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: spliceJunctionFile (66:9-66:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (534:5-534:25)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: statsFile (107:9-107:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (585:5-585:25)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (111:6-111:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (96:5-96:25)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (113:14-113:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_indexes (246:5-246:34)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (114:14-114:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bams (245:5-245:27)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (115:13-115:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_sample_alias (286:5-286:31)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (116:13-116:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf (284:5-284:20)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (117:16-117:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf (612:5-612:19)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (118:17-118:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf (668:5-668:19)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:17-119:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index (285:5-285:26)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (120:17-120:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index (613:5-613:25)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (121:17-121:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index (669:5-669:25)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (122:17-122:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: is_gvcf (622:5-622:27)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (123:17-123:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: is_gvcf (675:5-675:27)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (124:13-124:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: is_outlier_data (412:5-412:29)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (125:17-125:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lod_threshold (251:5-251:24)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (127:15-127:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (625:5-625:30)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (128:15-128:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_chimerism_in_reasonable_sample (358:5-358:45)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (132:13-132:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_duplication_in_reasonable_sample (357:5-357:47)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (133:16-133:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_output (410:5-410:20)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (159:14-159:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (212:5-212:30)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (160:14-160:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (414:5-414:30)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (161:14-161:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (499:5-499:30)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (162:14-162:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (541:5-541:30)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_size (299:5-299:27)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_basename (670:5-670:28)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_filename (22:5-22:28)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_filename (248:5-248:28)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:13-28:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_filename (454:5-454:28)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:13-31:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_filename (493:5-493:28)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:16-32:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_filename (537:5-537:28)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (46:14-46:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_prefix (145:5-145:29)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (70:6-70:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_prefix (51:5-51:29)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (72:14-72:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_prefix (97:5-97:29)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (73:16-73:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (292:5-292:27)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (76:13-76:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pre_adapter_detail_metrics (205:5-205:36)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (77:16-77:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (102:5-102:26)" +document = "biowdl/tasks:transcriptclean.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (89:14-89:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (150:5-150:26)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W002::Style/Medium] curly command found (38:5-47:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (211:5-211:26)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W002::Style/Medium] curly command found (97:5-108:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (24:5-24:30)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (111:14-111:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (250:5-250:26)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (112:14-112:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (300:5-300:30)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (113:15-113:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (360:5-360:30)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (114:15-114:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (413:5-413:30)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (115:15-115:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (459:5-459:26)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (498:5-498:26)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (52:5-52:26)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:15-26:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (540:5-540:26)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (587:5-587:26)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:17-28:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (621:5-621:30)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:16-29:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (676:5-676:26)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:17-30:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_group_md5_filename (586:5-586:35)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:17-31:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_length (458:5-458:26)" 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"[v1::W006::Naming/Low] identifier must be snake case (51:15-51:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (407:5-407:18)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (78:6-78:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (616:5-616:18)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (80:14-80:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (673:5-673:18)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (81:14-81:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (98:5-98:18)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (82:16-82:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (147:5-147:19)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (83:16-83:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (209:5-209:19)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (87:17-87:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (296:5-296:20)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (88:17-88:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (408:5-408:19)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (91:13-91:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (456:5-456:19)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (92:16-92:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (495:5-495:19)" +document = "biowdl/tasks:umi-tools.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (95:12-95:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (535:5-535:19)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (38:1-38:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (614:5-614:19)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (40:1-40:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (99:5-99:19)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W001::Style/Low] trailing space (26:79)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (100:5-100:25)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W001::Style/Low] trailing space (43:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (148:5-148:25)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (210:5-210:25)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:14-29:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (297:5-297:26)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:16-30:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (409:5-409:25)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:16-31:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (457:5-457:25)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:16-32:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (496:5-496:25)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:13-35:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (536:5-536:25)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:16-36:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (615:5-615:25)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (39:12-39:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: report_filename (406:5-406:27)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (82:14-82:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: target_interval_list (538:5-538:30)" +document = "biowdl/tasks:umi.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (83:14-83:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: total_input_size (249:5-249:27)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W002::Style/Medium] curly command found (72:5-117:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wgs_coverage_interval_list (455:5-455:36)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bcftoolsPath (61:9-61:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Qc.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wgs_coverage_interval_list (494:5-494:36)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2Path (55:9-55:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (116:1-116:2)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2buildPath (56:9-56:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (883:1-883:2)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination (64:9-64:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (949:1-949:2)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: depthFilter (44:9-44:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W001::Style/Low] trailing space (1013:19)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: existingLongReadAssembly (47:9-47:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W001::Style/Low] trailing space (1035:19)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: javaPath (59:9-59:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W001::Style/Low] trailing space (839:107)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: keep (34:9-34:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W001::Style/Low] trailing space (884:105)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kmerCount (43:9-43:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (1001:3-1006:4)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: linearSeqs (38:9-38:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (1026:3-1028:4)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: long (31:9-31:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (107:3-115:4)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lowScore (66:9-66:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (912:3-918:4)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: makeblastdbPath (52:9-52:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W002::Style/Medium] curly command found (943:3-948:4)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: maxKmerFrac (42:9-42:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: adapter_fasta (98:5-98:104)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory (69:9-69:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: aligned_bam (965:5-965:21)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minBridgeQual (37:9-37:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: alignment_summary_metrics (447:5-447:35)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minComponentSize (62:9-62:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (137:5-137:13)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minDeadEndSize (63:9-63:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (59:5-59:13)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minFastaLength (33:9-33:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (620:5-620:13)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minKmerFrac (41:9-41:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (663:5-663:13)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minPolishSize (60:9-60:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (905:5-905:13)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mode (36:9-36:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (9:5-9:14)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: noCorrect (40:9-40:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam_file (311:5-311:18)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: noMiniasm (45:9-45:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam_filename (201:5-201:24)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: noPilon (54:9-54:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam_index (621:5-621:19)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: noRotate (48:9-48:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam_with_readgroups (248:5-248:29)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: out (25:9-25:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam_without_readgroups (249:5-249:32)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pilonPath (58:9-58:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: base_name (848:5-848:21)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preCommand (27:9-27:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination (725:5-725:24)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: raconPath (46:9-46:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_error (726:5-726:30)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samtoolsPath (57:9-57:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (104:5-104:14)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: scores (65:9-65:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (141:5-141:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: short1 (28:9-28:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (14:5-14:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: short2 (29:9-29:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (209:5-209:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: spadesPath (39:9-39:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (252:5-252:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: startGeneCov (51:9-51:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (282:5-282:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: startGeneId (50:9-50:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (317:5-317:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: startGenes (49:9-49:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (363:5-363:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tblastnPath (53:9-53:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (403:5-403:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: threads (68:9-68:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (456:5-456:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unpaired (30:9-30:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (545:5-545:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (35:9-35:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (588:5-588:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: verbosity (32:9-32:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (625:5-625:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (120:14-120:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (64:5-64:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (121:14-121:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (669:5-669:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (730:5-730:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:17-27:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (805:5-805:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:15-28:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (856:5-856:16)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:15-29:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (1021:5-1021:27)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:14-33:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (102:5-102:57)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:16-37:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (143:5-143:83)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:14-38:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (16:5-16:98)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (39:15-39:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (211:5-211:88)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (40:18-40:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (254:5-254:99)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:16-41:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (284:5-284:57)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (42:16-42:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (319:5-319:105)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (43:14-43:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (365:5-365:137)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (44:16-44:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (405:5-405:137)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (45:18-45:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (458:5-458:26)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (46:15-46:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (547:5-547:84)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (47:15-47:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (590:5-590:84)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (48:18-48:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (627:5-627:71)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (49:15-49:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (66:5-66:57)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:16-50:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (671:5-671:55)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (51:16-51:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (732:5-732:26)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (52:17-52:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (807:5-807:26)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (53:15-53:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (858:5-858:27)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (54:18-54:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (909:5-909:54)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (55:15-55:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (938:5-938:63)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (56:15-56:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (970:5-970:94)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (57:15-57:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (996:5-996:59)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (58:15-58:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (100:5-100:78)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (59:15-59:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (1022:5-1022:56)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (60:14-60:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (13:5-13:76)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (61:15-61:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (140:5-140:92)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (62:14-62:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (208:5-208:67)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (63:14-63:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (251:5-251:79)" +document = "biowdl/tasks:unicycler.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (66:17-66:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (281:5-281:56)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W002::Style/Medium] curly command found (56:5-81:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (316:5-316:141)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: vcfFile (123:9-123:16)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (362:5-362:70)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:6-25:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (402:5-402:68)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (455:5-455:39)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:14-28:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (544:5-544:69)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:14-29:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (587:5-587:69)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:14-30:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (624:5-624:81)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:14-31:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (63:5-63:77)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:14-32:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (668:5-668:70)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:16-33:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (855:5-855:56)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:17-34:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (907:5-907:69)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:17-35:48)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (936:5-936:59)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:15-36:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (968:5-968:56)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:13-37:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (997:5-997:56)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:13-38:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_metrics (450:5-450:27)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (39:15-39:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_metrics (706:5-706:29)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (40:13-40:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: exon_bed (314:5-314:18)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:13-41:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq1 (95:5-95:16)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (42:13-42:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq2 (96:5-96:16)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (43:13-43:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqc_html_report (727:5-727:30)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (45:17-45:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqc_percent_reads_with_adapter (728:5-728:45)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (46:15-46:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fingerprint_summary_metrics (452:5-452:38)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (47:15-47:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genes_gtf (312:5-312:19)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (49:16-49:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (352:5-352:19)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (52:13-52:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (394:5-394:19)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (53:16-53:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (536:5-536:19)" +document = "biowdl/tasks:vardict.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (84:14-84:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (579:5-579:19)" +document = "biowdl/tasks:vt.wdl" +message = "[v1::W002::Style/Medium] curly command found (37:5-44:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (995:5-995:19)" +document = "biowdl/tasks:vt.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: outputVcf (69:9-69:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (353:5-353:25)" +document = "biowdl/tasks:vt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (395:5-395:25)" +document = "biowdl/tasks:vt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: insert_size_metrics (448:5-448:29)" +document = "biowdl/tasks:vt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: library_name (202:5-202:24)" +document = "biowdl/tasks:vt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:14-27:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mem (935:5-935:19)" +document = "biowdl/tasks:vt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:14-28:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (101:5-101:58)" +document = "biowdl/tasks:vt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:17-29:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (1023:5-1023:25)" +document = "biowdl/tasks:vt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:16-30:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (142:5-142:63)" +document = "biowdl/tasks:vt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:13-33:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (15:5-15:25)" +document = "biowdl/tasks:vt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:16-34:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (210:5-210:25)" +document = "biowdl/tasks:vt.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (47:14-47:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (253:5-253:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W002::Style/Medium] curly command found (118:5-126:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (283:5-283:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W002::Style/Medium] curly command found (178:5-189:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (318:5-318:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W002::Style/Medium] curly command found (47:5-63:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (364:5-364:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: bam (218:9-218:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (404:5-404:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: bamIndex (219:9-219:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (457:5-457:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: phasedBlockList (155:9-155:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (546:5-546:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: phasedGTF (153:9-153:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (589:5-589:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: phasedTSV (154:9-154:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (626:5-626:26)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: phasedVCF (97:9-97:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (65:5-65:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: phasedVCFIndex (98:9-98:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (670:5-670:26)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (102:6-102:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (731:5-731:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (109:17-109:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (806:5-806:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (113:13-113:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (857:5-857:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (115:16-115:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (908:5-908:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (129:15-129:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (937:5-937:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (130:15-130:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (969:5-969:26)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (131:15-131:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (998:5-998:26)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (159:6-159:14)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (103:5-103:96)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (162:14-162:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: monitoring_script (629:5-629:96)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (164:14-164:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam (704:5-704:22)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (165:16-165:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (537:5-537:31)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (168:15-168:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (580:5-580:31)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (173:13-173:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (622:5-622:31)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (175:16-175:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_index (705:5-705:28)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (193:14-193:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_prefix (354:5-354:29)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_prefix (396:5-396:29)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:16-25:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (453:5-453:27)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:14-27:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (664:5-664:27)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:14-28:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (967:5-967:27)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:14-29:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_prefix (906:5-906:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:15-32:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_prefix (97:5-97:25)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (42:13-42:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputs_json (803:5-803:22)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (44:16-44:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_alignment_summary_metrics (713:5-713:44)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (66:14-66:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_base_distribution_by_cycle_metrics (716:5-716:53)" +document = "biowdl/tasks:whatshap.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (67:14-67:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_base_distribution_by_cycle_pdf (717:5-717:49)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W002::Style/Medium] curly command found (115:5-125:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_fingerprint_detail_metrics (723:5-723:46)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W002::Style/Medium] curly command found (154:5-164:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_fingerprint_summary_metrics (722:5-722:47)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W002::Style/Medium] curly command found (38:5-47:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_insert_size_histogram (715:5-715:40)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W002::Style/Medium] curly command found (76:5-88:6)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_insert_size_metrics (714:5-714:38)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binFile (108:9-108:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_quality_by_cycle_metrics (718:5-718:43)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binFile (148:9-148:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_quality_by_cycle_pdf (719:5-719:39)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binFile (32:9-32:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_quality_distribution_metrics (720:5-720:47)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binFile (67:9-67:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_quality_distribution_pdf (721:5-721:43)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binSize (107:9-107:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_rna_metrics (449:5-449:28)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binSize (147:9-147:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_rna_metrics (712:5-712:30)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binSize (31:9-31:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: platform (203:5-203:20)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: binSize (66:9-66:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: platform_unit (204:5-204:25)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dictionaryFile (143:9-143:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: population_vcf (852:5-852:24)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dictionaryFileIndex (144:9-144:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: population_vcf_index (853:5-853:30)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dockerImage (112:9-112:83)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (994:5-994:18)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dockerImage (151:9-151:83)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r1_fastq (10:5-10:19)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dockerImage (35:9-35:83)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r1_fastq (199:5-199:18)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dockerImage (73:9-73:83)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r2_fastq (11:5-11:19)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fracLowess (70:9-70:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r2_fastq (200:5-200:18)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fracN (68:9-68:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read1Structure (60:5-60:26)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: inputBam (25:9-25:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read2Structure (61:5-61:26)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: inputBamIndex (26:9-26:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_group_name (205:5-205:27)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: inputBed (141:9-141:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (355:5-355:18)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: inputBed (63:9-63:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (397:5-397:18)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: inputBedIndex (142:9-142:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (356:5-356:19)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: inputBeds (104:9-104:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (398:5-398:19)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: iter (69:9-69:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (357:5-357:25)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory (111:9-111:56)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (399:5-399:25)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory (150:9-150:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_flat (358:5-358:18)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory (34:9-34:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: remove_duplicates (665:5-665:30)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory (72:9-72:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ribosomal_intervals (359:5-359:29)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nBins (109:9-109:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rnaseqc2_exon_counts (709:5-709:32)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputBed (105:9-105:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rnaseqc2_fragment_size_histogram (710:5-710:44)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputBed (145:9-145:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rnaseqc2_gene_counts (708:5-708:32)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputBed (29:9-29:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rnaseqc2_gene_tpm (707:5-707:29)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputBed (64:9-64:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rnaseqc2_metrics (451:5-451:26)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference (102:9-102:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rnaseqc2_metrics (711:5-711:28)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference (139:9-139:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_id (313:5-313:21)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference (27:9-27:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_id (701:5-701:21)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference (61:9-61:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sequencing_center (206:5-206:29)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: referenceIndex (103:9-103:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sort_sam_disk_multiplier (541:5-541:41)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: referenceIndex (140:9-140:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sort_sam_disk_multiplier (584:5-584:41)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: referenceIndex (28:9-28:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: starIndex (138:5-138:19)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: referenceIndex (62:9-62:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tdr_dataset_uuid (802:5-802:28)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (100:6-100:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: transcriptome_bam (702:5-702:29)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (103:14-103:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: transcriptome_duplicate_metrics (703:5-703:43)" 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"[v1::W006::Naming/Low] identifier must be snake case (128:14-128:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within workflow: coordinate_sort (35:5-35:20)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (137:6-137:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UMIAwareDuplicateMarking.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: coordinate_sort_output (27:5-27:35)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (140:14-140:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (77:1-77:12)" +document = 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"[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (235:5-235:18)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:6-23:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (291:5-291:18)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:14-25:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (328:5-328:18)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:14-26:27)" [[concerns]] kind = "LintWarning" -document = 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(31:14-31:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (146:9-146:95)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:15-32:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (182:9-182:95)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:16-35:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (236:5-236:91)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:14-50:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (292:5-292:91)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (59:6-59:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (329:5-329:56)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (62:14-62:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (387:9-387:60)" 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missing parameter meta within task: h5_input (289:5-289:18)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (67:15-67:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf (120:9-120:23)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (68:16-68:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf (145:9-145:23)" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (70:16-70:26)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (73:16-73:27)" + +[[concerns]] +kind = "LintWarning" +document = "biowdl/tasks:wisestork.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (91:14-91:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bait_interval_list (29:5-29:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bait_set_name (30:5-30:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: 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missing parameter meta within task: docker (486:9-486:78)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (547:9-547:78)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (650:9-650:78)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (701:9-701:78)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (747:9-747:78)" + +[[concerns]] +kind = "LintWarning" +document = 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missing parameter meta within task: min_read_length (248:9-248:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (411:9-411:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (483:9-483:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: name_sorted_bam (744:9-744:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: num_downstr_bases (858:9-858:30)" + 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missing parameter meta within task: plate_id (648:9-648:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: plate_id (699:9-699:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: plate_id (745:9-745:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: plate_id (799:8-799:23)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:beta-pipelines/skylab/m3c/CondensedSnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: plate_id (856:9-856:24)" + +[[concerns]] +kind = "LintWarning" +document = 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missing parameter meta within task: max_retries (291:9-291:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (345:9-345:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (391:5-391:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (448:9-448:28)" + +[[concerns]] +kind = "LintWarning" +document = 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missing parameter meta within task: memory_multiplier (399:5-399:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outbam (387:5-387:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_prefix (596:5-596:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputdir (86:9-86:31)" + +[[concerns]] +kind = "LintWarning" +document = 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"[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (344:9-344:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (447:9-447:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (499:9-499:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (551:9-551:28)" + +[[concerns]] +kind = "LintWarning" +document = 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_vcf (30:5-30:20)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_vcf_index (31:5-31:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_basename (47:5-47:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read_fingerprint_from_mercury (40:5-40:50)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (51:5-51:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (49:5-49:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (50:5-50:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_alias (45:5-45:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/qc/CheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_lsid (44:5-44:24)" + +[[concerns]] +kind = "LintWarning" +document = 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"broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (145:5-145:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (179:5-179:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (212:5-212:23)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (240:5-240:18)" + +[[concerns]] +kind = "LintWarning" 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"LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (266:5-266:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (300:5-300:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_in_MiB (104:5-104:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_in_MiB (146:5-146:29)" + 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memory_in_MiB (269:5-269:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_in_MiB (302:5-302:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_filename (102:5-102:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_filename (301:5-301:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (144:5-144:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_group_map_file (211:5-211:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (141:5-141:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (142:5-142:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: report_filename (267:5-267:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rg_to_ubam_file (239:5-239:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sort_sam_disk_multiplier (303:5-303:39)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unmapped_bam_suffix (178:5-178:31)" + +[[concerns]] +kind = "LintWarning" +document = 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(21:5-21:49)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (104:9-104:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (10:10-10:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (139:6-139:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (146:9-146:22)" + +[[concerns]] +kind = "LintWarning" +document = 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parameter meta within workflow: fastq_r1_gzipped_input (10:7-10:34)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_r2_gzipped_input (11:7-11:34)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fwd_bowtie2_index_files (30:7-30:42)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fwd_converted_reference_fasta (28:7-28:41)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:pipelines/cemba/cemba_methylcseq/CEMBA.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: 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library (102:5-102:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: links_objects (574:5-574:32)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (111:5-111:66)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (151:5-151:88)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (15:5-15:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (205:5-205:59)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (243:5-243:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (290:5-290:56)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (373:5-373:56)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (421:5-421:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (457:5-457:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (484:5-484:59)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (515:5-515:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (547:5-547:80)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (584:5-584:26)" 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parameter meta within task: memory_mb (742:5-742:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ncbi_taxon_id (414:5-414:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: organ (104:5-104:17)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (107:5-107:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_file_path (272:5-272:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_looms (101:5-101:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_path (63:5-63:23)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (141:5-141:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (196:5-196:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (236:5-236:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (271:5-271:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (365:5-365:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (413:5-413:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_type (480:5-480:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (238:5-238:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (644:5-644:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (645:5-645:42)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: process_input_ids (276:5-276:36)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_id (105:5-105:22)" + +[[concerns]] +kind = "LintWarning" 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project_level (273:5-273:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_loom (145:5-145:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_name (106:5-106:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (510:5-510:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_file_descriptor_objects (577:5-577:52)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_metadata_objects (576:5-576:45)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_type (415:5-415:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_version (417:5-417:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: references (198:5-198:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: species (103:5-103:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: species (511:5-511:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ss2_bai_file (147:5-147:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ss2_bam_file (146:5-146:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ss2_index (201:5-201:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: staging_area (737:5-737:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: staging_bucket (579:5-579:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: version_timestamp (142:5-142:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: version_timestamp (197:5-197:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: version_timestamp (237:5-237:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: version_timestamp (275:5-275:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: version_timestamp (367:5-367:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: version_timestamp (416:5-416:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (138:6-138:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (146:13-146:25)" 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"[v1::W006::Naming/Low] identifier must be snake case (477:6-477:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (508:6-508:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (541:6-541:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (568:6-568:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (61:6-61:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/AdapterTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (642:6-642:31)" + 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: version_timestamp (14:5-14:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:projects/tasks/CreateReferenceMetadata.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (5:10-5:33)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W002::Style/Medium] curly command found (275:3-277:4)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (273:5-273:88)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: expressions (108:5-108:30)" + +[[concerns]] +kind = "LintWarning" +document = 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(107:5-107:17)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: mem (240:9-240:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: original_vcf (270:5-270:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: original_vcf_index (271:5-271:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (105:5-105:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (272:5-272:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (106:5-106:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (103:5-103:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (104:5-104:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tables (239:9-239:27)" + +[[concerns]] +kind = "LintWarning" 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(12:9-12:47)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: thousandG_vcf (6:9-6:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (12:23-12:47)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (130:6-130:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (159:6-159:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/BuildAFComparisonTable.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (183:6-183:19)" + +[[concerns]] 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must be snake case (110:13-110:23)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (111:13-111:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (138:14-138:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (139:14-139:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (140:14-140:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (141:14-141:28)" + +[[concerns]] +kind = "LintWarning" 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"[v1::W006::Naming/Low] identifier must be snake case (252:6-252:20)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (278:6-278:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (280:10-280:17)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (4:10-4:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:scripts/RemoveBadSitesByID.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (7:14-7:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:structs/imputation/ImputationStructs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (8:7-8:12)" + 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(30:5-30:44)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_name (27:5-27:23)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (22:10-22:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/AggregatedBamQC.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (90:10-90:43)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W002::Style/Medium] curly command found (141:3-152:4)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: allow_empty_ref_alt (36:5-36:40)" + +[[concerns]] +kind 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input_bam (130:5-130:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (23:5-23:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: n_reads (131:5-131:16)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (25:5-25:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (133:5-133:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (33:5-33:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_fasta (30:5-30:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unmap_contaminant_reads (35:5-35:43)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (128:6-128:17)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (21:6-21:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W002::Style/Medium] curly command found (150:3-162:4)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W002::Style/Medium] curly command found (210:3-228:4)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W002::Style/Medium] curly command found (251:3-256:6)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W002::Style/Medium] curly command found (287:3-294:6)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W002::Style/Medium] curly command found (322:3-329:6)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W002::Style/Medium] curly command found (37:3-47:4)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W002::Style/Medium] curly command found (95:3-108:4)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_disk (191:5-191:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_disk (25:5-25:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_disk (277:5-277:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: additional_disk (78:5-78:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bait_set_name (343:5-343:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bin_base_qualities (192:5-192:38)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bqsr_scatter (135:5-135:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bqsr_scatter (187:5-187:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (186:5-186:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (24:5-24:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (275:5-275:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (315:5-315:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (70:5-70:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_sites_bed (346:5-346:33)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_sites_bed (411:5-411:33)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_sites_mu (347:5-347:32)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_sites_mu (412:5-412:32)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contamination_sites_ud (345:5-345:32)" + 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"[v1::W003::Completeness/Medium] missing parameter meta within task: disable_sanity_check (418:5-418:41)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (420:6-420:121)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (137:5-137:61)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (189:5-189:61)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (248:5-248:61)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (21:5-21:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (408:5-408:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (125:5-125:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index (179:5-179:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam_index 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"[v1::W003::Completeness/Medium] missing parameter meta within task: known_indels_sites_indices (131:5-131:43)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: known_indels_sites_vcfs (130:5-130:40)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (190:5-190:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (26:5-26:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (278:5-278:30)" + +[[concerns]] 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parameter meta within task: output_bam_basename (273:5-273:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (313:5-313:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (67:5-67:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_prefix (415:5-415:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_report_filename (246:5-246:34)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (136:5-136:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (188:5-188:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (23:5-23:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (247:5-247:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (276:5-276:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (316:5-316:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (348:5-348:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (416:5-416:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (71:5-71:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" 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"LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (133:5-133:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (184:5-184:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (413:5-413:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (134:5-134:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (185:5-185:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (414:5-414:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sequence_group_interval (127:5-127:42)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sequence_group_interval (182:5-182:42)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: somatic (193:5-193:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/BamProcessing.wdl" 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cpu (879:5-879:16)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dataset_bcf (182:5-182:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dataset_bcf_index (183:5-183:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (118:5-118:96)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (11:5-11:57)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (150:5-150:89)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (194:5-194:132)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (231:5-231:85)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (272:5-272:55)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (338:5-338:80)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (36:5-36:57)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (374:5-374:93)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (404:5-404:94)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (438:5-438:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (471:5-471:95)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (510:5-510:52)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (535:5-535:57)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (583:5-583:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (620:5-620:56)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (659:5-659:53)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (65:5-65:53)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (708:5-708:58)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (732:5-732:54)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (760:5-760:56)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (798:5-798:56)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (826:5-826:57)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (857:5-857:77)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (883:5-883:89)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: eagle_docker (191:5-191:92)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: end (189:5-189:12)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: end (225:5-225:12)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: end (59:5-59:12)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: end (656:5-656:12)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ends (574:5-574:20)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: exclude_filtered (657:5-657:37)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file1 (851:5-851:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file2 (852:5-852:15)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (115:5-115:61)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (269:5-269:61)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (339:5-339:61)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (375:5-375:61)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (662:5-662:61)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gatk_docker (68:5-68:61)" + +[[concerns]] +kind = "LintWarning" +document = 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parameter meta within task: memory_mb (534:5-534:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (582:5-582:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (619:5-619:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (661:5-661:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (67:5-67:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" 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missing parameter meta within task: optional_qc_max_missing (432:5-432:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: original_vcf (370:5-370:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: original_vcf (400:5-400:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: original_vcf_index (371:5-371:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/ImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: original_vcf_index (401:5-401:28)" + +[[concerns]] +kind = "LintWarning" +document = 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"broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: authentication (47:5-47:33)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: autocall_version (9:5-9:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: baf_regress_metrics_file (498:9-498:41)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bafregress_metrics (177:5-177:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bpm_filename (428:5-428:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bpm_filename (461:5-461:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_type (7:5-7:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_type_name (294:5-294:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcode (295:5-295:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcode (389:5-389:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcode (43:5-43:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcode (5:5-5:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcode_output (496:9-496:41)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_filename (11:5-11:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: collaborator_participant_id (296:5-296:40)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (144:5-144:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (183:5-183:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (251:5-251:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (356:5-356:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (89:5-89:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: egt_filename (429:5-429:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: extended_manifest_map_file (427:5-427:36)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fingerprint_detail_metrics_file (508:9-508:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fingerprint_summary_metrics_file (509:9-509:49)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fingerprinting_detail_metrics (171:5-171:40)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fingerprinting_summary_metrics (172:5-172:41)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gender (307:5-307:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_contingency_metrics (175:5-175:51)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_contingency_metrics_file (513:9-513:62)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_detail_metrics (174:5-174:46)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_detail_metrics_file (512:9-512:57)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_summary_metrics (173:5-173:47)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genotype_concordance_summary_metrics_file (511:9-511:58)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gtc_file (499:9-499:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (141:5-141:20)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_file (84:5-84:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index_file (85:5-85:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lab_batch (297:5-297:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lab_batch (515:9-515:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minor_allele_frequency_map_file (460:5-460:41)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: notes (50:5-50:17)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_json_filename (88:5-88:32)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_metrics_basefilename (142:5-142:39)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_metrics_basename (10:5-10:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf (501:9-501:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_vcf_index (502:9-502:33)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: params_file (352:5-352:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: participant_id (298:5-298:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (13:5-13:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (145:5-145:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (184:5-184:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (252:5-252:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (310:5-310:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (357:5-357:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (390:5-390:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (431:5-431:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (45:5-45:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (463:5-463:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (90:5-90:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: product_family (299:5-299:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: product_name (300:5-300:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: product_order_id (301:5-301:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: product_part_number (302:5-302:32)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: product_type (303:5-303:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reason (49:5-49:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: regulatory_designation (304:5-304:34)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reported_gender (8:5-8:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: research_project_id (305:5-305:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_alias (306:5-306:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_alias (6:5-6:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_id (308:5-308:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_lsid (309:5-309:23)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_lsid (87:5-87:23)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: service_account_filename (181:5-181:36)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: service_account_filename (249:5-249:36)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: service_account_filename (355:5-355:36)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: service_account_filename (393:5-393:36)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: service_account_filename (48:5-48:36)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: upload_metrics_output (42:5-42:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: variant_calling_detail_metrics_file (86:5-86:45)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vault_token_path (179:5-179:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vault_token_path (247:5-247:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vault_token_path (353:5-353:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vault_token_path (391:5-391:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vault_token_path (46:5-46:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: verify_id_metrics (176:5-176:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (139:6-139:33)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (166:6-166:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (243:6-243:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (292:6-292:37)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (350:6-350:32)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (387:6-387:42)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:44)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (40:6-40:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (425:6-425:41)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (458:6-458:37)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (494:6-494:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalArraysTasks.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (82:6-82:33)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (140:1-140:8)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: aggregated_imputation_metrics (5:9-5:54)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chip_well_barcodes (12:9-12:43)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chunks_info (6:9-6:36)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: failed_chunks (7:9-7:38)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: imputation_outputs_tsv (130:9-130:47)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: imputed_multisample_vcf (8:9-8:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: imputed_multisample_vcf_index (9:9-9:54)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: imputed_single_sample_vcf_indices (11:9-11:58)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: imputed_single_sample_vcf_indices (63:9-63:58)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/InternalImputationTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta 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missing parameter meta within task: hapmap_resource_vcf_index (398:5-398:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hapmap_resource_vcf_index (463:5-463:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: indel_filter_level (605:5-605:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: indels_recalibration (599:5-599:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/JointGenotypingTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: indels_recalibration_index (600:5-600:36)" + 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meta within task: memory_multiplier (212:5-212:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (414:5-414:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (499:5-499:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_multiplier (541:5-541:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_size (299:5-299:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_basename (673:5-673:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_filename (22:5-22:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_filename (248:5-248:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_filename (454:5-454:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_filename (493:5-493:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_filename (537:5-537:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_prefix (145:5-145:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_prefix (51:5-51:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_prefix (97:5-97:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (292:5-292:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pre_adapter_detail_metrics (205:5-205:36)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (102:5-102:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (150:5-150:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (211:5-211:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (24:5-24:30)" + +[[concerns]] 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task: preemptible_tries (622:5-622:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (679:5-679:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_group_md5_filename (586:5-586:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_length (458:5-458:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_length (497:5-497:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/Qc.wdl" +message = "[v1::W003::Completeness/Medium] missing 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missing parameter meta within task: cpu (625:5-625:16)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (64:5-64:16)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (669:5-669:16)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (730:5-730:16)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (805:5-805:16)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = 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"broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (546:5-546:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (589:5-589:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (626:5-626:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (65:5-65:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb 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parameter meta within task: output_bam_index (705:5-705:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_prefix (354:5-354:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_prefix (396:5-396:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (453:5-453:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/RNAWithUMIsTasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (664:5-664:27)" + +[[concerns]] +kind = "LintWarning" +document = 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contains only whitespace (77:1-77:12)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W001::Style/Low] trailing space (159:77)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W001::Style/Low] trailing space (322:10)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W001::Style/Low] trailing space (8:39)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotation_intervals (234:5-234:37)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = 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missing parameter meta within task: disk_size (235:5-235:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (291:5-291:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (328:5-328:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (386:9-386:61)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb 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"broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (112:14-112:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (117:6-117:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (143:6-143:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (177:6-177:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (215:6-215:26)" 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"[v1::W006::Naming/Low] identifier must be snake case (321:6-321:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (381:6-381:23)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (8:10-8:37)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsWholeGenomeGermlineQC.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: agg_bam (8:5-8:17)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/broad/UltimaGenomicsWholeGenomeGermlineQC.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: agg_bam_index (9:5-9:23)" + +[[concerns]] +kind = "LintWarning" +document = 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"broadinstitute/warp:tests/skylab/smartseq2_single_nucleus/pr/test_smartseq2_single_nucleus_PR.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tar_star_reference (19:5-19:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tests/skylab/smartseq2_single_nucleus/pr/test_smartseq2_single_nucleus_PR.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_bam (13:5-13:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tests/skylab/smartseq2_single_nucleus/pr/test_smartseq2_single_nucleus_PR.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_exon_intron_counts_hash (12:5-12:48)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tests/skylab/smartseq2_single_nucleus/pr/test_smartseq2_single_nucleus_PR.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_loom (14:5-14:20)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tests/skylab/smartseq2_single_nucleus/pr/test_smartseq2_single_nucleus_PR.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (24:17-24:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tests/skylab/smartseq2_single_nucleus/pr/test_smartseq2_single_nucleus_PR.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:17-25:35)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tests/skylab/smartseq2_single_nucleus/pr/test_smartseq2_single_nucleus_PR.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (8:10-8:38)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bead_pool_manifest_file (29:5-29:33)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (46:5-46:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_fp_vcf (35:5-35:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_green_idat_md5 (41:5-41:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gtc (27:5-27:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (25:5-25:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_params_file (44:5-44:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_red_idat_md5 (38:5-38:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_vcf (32:5-32:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_fp_vcf (34:5-34:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_green_idat_md5 (40:5-40:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gtc (28:5-28:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (24:5-24:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_params_file (43:5-43:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_red_idat_md5 (37:5-37:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf (31:5-31:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (22:10-22:22)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:10-37:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:10-38:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (40:10-40:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyArrays.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:10-41:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (31:5-31:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_fingerprint_vcf (28:5-28:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (25:5-25:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_fingerprint_vcf (29:5-29:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (26:5-26:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (22:10-22:32)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBams.wdl" +message = "[v1::W002::Style/Medium] curly command found (38:3-43:4)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_bam (31:5-31:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_bam (32:5-32:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bam_pairs (7:5-7:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBams.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:6-28:17)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBams.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (4:10-4:34)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" +message = "[v1::W002::Style/Medium] curly command found (35:3-40:4)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_bam (28:5-28:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_bam (29:5-29:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (9:5-9:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_bam (8:5-8:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_bam (7:5-7:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:6-25:17)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (4:10-4:34)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W002::Style/Medium] curly command found (69:3-74:4)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_bam (62:5-62:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_bam (63:5-63:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (24:5-24:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_bams (21:5-21:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_crai (14:5-14:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_cram (13:5-13:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gvcf (18:5-18:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gvcf_index (19:5-19:25)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (9:5-9:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_bams (22:5-22:27)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_crai (12:5-12:20)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_cram (11:5-11:20)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gvcf (16:5-16:20)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gvcf_index (17:5-17:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (8:5-8:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (59:6-59:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (5:10-5:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" +message = "[v1::W001::Style/Low] trailing space (26:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" +message = "[v1::W002::Style/Medium] curly command found (24:5-32:6)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: destination_cloud_path (21:9-21:38)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: done (20:9-20:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: destination_cloud_path (7:9-7:38)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (6:9-6:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (18:6-18:16)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (3:10-3:36)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGDCSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (17:5-17:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGDCSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_bai (15:5-15:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGDCSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_bam (14:5-14:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGDCSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (10:5-10:29)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGDCSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_bai (13:5-13:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGDCSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_bam (12:5-12:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGDCSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (9:5-9:30)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGDCSomaticSingleSample.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (6:10-6:38)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGermlineSingleSample.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (98:1-98:2)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGermlineSingleSample.wdl" +message = "[v1::W001::Style/Low] trailing space (22:18)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGermlineSingleSample.wdl" +message = "[v1::W002::Style/Medium] curly command found (77:3-90:4)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (74:5-74:87)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/VerifyGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_gvcf (72:5-72:19)" + +[[concerns]] +kind = "LintWarning" +document = 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task: input_vcf_index (220:5-220:25)" +document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: additional_disk (19:7-19:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index (325:5-325:25)" +document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (17:7-17:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_vcf_index (384:9-384:29)" +document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" +message 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"LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (385:9-385:31)" +document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_map (16:7-16:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (231:5-231:18)" +document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (14:7-14:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (390:9-390:22)" +document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (15:7-15:28)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (23:7-23:26)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (22:7-22:24)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unmapped_bam_suffix (18:7-18:51)" + +[[concerns]] +kind = "LintWarning" 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (30:5-30:37)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: papi_settings (11:5-11:31)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: provide_bam_output (23:5-23:39)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: references (13:5-13:44)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" +message = 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"LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: final_gvcf_base_name (20:5-20:32)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_file (31:5-31:37)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_index (32:5-32:38)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (42:5-42:37)" + +[[concerns]] +kind = "LintWarning" 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta_index (20:7-20:32)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: destination_cloud_path (28:7-28:36)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: final_gvcf_base_name (17:7-17:34)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_file (22:7-22:39)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_index (23:7-23:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (230:5-230:19)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (35:7-35:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (388:9-388:23)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (13:7-13:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (389:9-389:29)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram (12:7-12:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_sdf (232:5-232:23)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_map (14:7-14:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: runs_file (229:5-229:19)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: papi_settings (26:7-26:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_name (119:9-119:27)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: references (24:7-24:46)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: score_key (293:5-293:21)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (32:7-32:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: score_key (327:5-327:21)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_name (15:7-15:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: thresholds (323:5-323:20)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: scatter_settings (25:7-25:53)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_highconf (226:5-226:24)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (31:7-31:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_sample_name (218:5-218:29)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unmapped_bam_suffix (18:7-18:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_vcf (224:5-224:19)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (33:7-33:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_vcf_index (225:5-225:25)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (34:7-34:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: annotation_intervals (24:9-24:41)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: wgs_coverage_interval_list (21:7-21:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (12:9-12:30)" +document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:45)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: call_sample_name (13:9-13:32)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (102:1-102:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: flow_order (18:9-18:26)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (44:1-44:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_vcf (10:9-10:30)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (90:1-90:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_vcf_index (11:9-11:36)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (92:1-92:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: medium_disk (26:9-26:24)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W001::Style/Low] trailing space (106:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (21:9-21:22)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W001::Style/Low] trailing space (137:50)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (19:9-19:23)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W001::Style/Low] trailing space (139:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (20:9-20:29)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W001::Style/Low] trailing space (141:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_sdf (22:9-22:27)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W001::Style/Low] trailing space (49:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: runs_file (23:9-23:23)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (18:7-18:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: score_key (25:9-25:35)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_vcf (20:7-20:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_highconf_intervals (16:9-16:38)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_vcf_index (21:7-21:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_sample_name (17:9-17:33)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta (14:7-14:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf (14:9-14:23)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta_index (15:7-15:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf_index (15:9-15:29)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf (22:7-22:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsWholeGenomeGermlineQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: agg_bam (8:5-8:17)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf_index (23:7-23:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsWholeGenomeGermlineQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: agg_bam_index (9:5-9:23)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (38:7-38:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsWholeGenomeGermlineQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (10:5-10:26)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (13:7-13:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsWholeGenomeGermlineQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name_sub (11:5-11:30)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram (12:7-12:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsWholeGenomeGermlineQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_sites (14:5-14:43)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_map (16:7-16:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsWholeGenomeGermlineQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: flow_order (19:5-19:22)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_amb (27:7-27:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsWholeGenomeGermlineQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_chimerism_in_reasonable_sample (18:5-18:45)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_ann (28:7-28:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsWholeGenomeGermlineQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_duplication_in_reasonable_sample (17:5-17:47)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_bwt (29:7-29:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsWholeGenomeGermlineQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: references (13:5-13:26)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (26:7-26:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UltimaGenomicsWholeGenomeGermlineQC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: wgs_coverage_interval_list (15:5-15:36)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fai (25:7-25:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: allow_empty_ref_alt (50:5-50:40)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (24:7-24:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bin_base_qualities (46:5-46:38)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_pac (30:7-30:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_sites_bed (37:5-37:33)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_sa (31:7-31:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_sites_mu (38:5-38:32)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (35:7-35:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_sites_ud (36:5-36:32)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (34:7-34:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cross_check_fingerprints_by (40:5-40:39)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ubam (19:7-19:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dragmap_reference (33:5-33:40)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unmapped_bam_suffix (17:7-17:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database_file (41:5-41:33)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (36:7-36:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hard_clip_reads (44:5-44:36)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (37:7-37:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lod_threshold (42:5-42:24)" +document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:47)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: papi_settings (34:5-34:31)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (111:1-111:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: perform_bqsr (48:5-48:32)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (137:1-137:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: recalibrated_bam_basename (43:5-43:37)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (206:1-206:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: references (32:5-32:44)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (56:1-56:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_and_unmapped_bams (31:5-31:51)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (91:1-91:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: somatic (47:5-47:28)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (94:1-94:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unmap_contaminant_reads (45:5-45:43)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] trailing space (141:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/UnmappedBamToAlignedBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_bwa_mem (49:5-49:31)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] trailing space (191:50)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: break_bands_at_multiples_of (81:5-81:36)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] trailing space (193:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (233:5-233:16)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] trailing space (195:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (128:5-128:116)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] trailing space (197:46)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (235:5-235:26)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] trailing space (199:57)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (232:5-232:76)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W001::Style/Low] trailing space (201:61)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_bam (122:5-122:19)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: analysis_version_number (13:7-13:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_cram (163:5-163:20)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bead_pool_manifest_file (24:7-24:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (230:5-230:23)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: call_rate_threshold (14:7-14:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_files (229:5-229:31)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chip_type (25:7-25:67)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: interval_list (79:5-79:23)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chip_well_barcode (16:7-16:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (234:5-234:25)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cluster_file (27:7-27:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: message (212:5-212:19)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_controls_vcf (35:7-35:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (125:5-125:27)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: control_sample_intervals_file (39:7-39:42)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_basename (166:5-166:27)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: control_sample_name (40:7-40:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (126:5-126:30)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: control_sample_vcf_file (37:7-37:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (194:5-194:26)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: control_sample_vcf_index_file (38:7-38:42)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible_tries (22:5-22:26)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbSNP_vcf (22:7-22:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_dict (21:5-21:18)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbSNP_vcf_index (23:7-23:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (123:5-123:19)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: disk_size (41:7-41:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (164:5-164:19)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: extended_chip_manifest_file (26:7-26:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (124:5-124:25)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_vcf_file (30:7-30:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta_index (165:5-165:25)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_vcf_index_file (31:7-31:49)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: results_path (227:5-227:24)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gender_cluster_file (28:7-28:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: scatter_count (80:5-80:22)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genotype_concordance_threshold (43:7-43:50)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sizes (193:5-193:23)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (50:7-50:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/broad/Utilities.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_path (228:5-228:22)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: green_idat_cloud_path (18:7-18:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Attach10xBarcodes.wdl" -message = "[v1::W002::Style/Medium] curly command found (38:3-70:4)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database_file (32:7-32:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (126:1-126:4)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minor_allele_frequency_file (36:7-36:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (80:1-80:4)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: preemptible_tries (42:7-42:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W001::Style/Low] trailing space (161:4)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: red_idat_cloud_path (17:7-17:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W001::Style/Low] trailing space (69:5)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (21:7-21:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W002::Style/Medium] curly command found (22:3-43:4)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (19:7-19:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_exons (61:5-61:24)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (20:7-20:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counting_mode (59:5-59:25)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reported_gender (15:7-15:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (64:5-64:16)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (47:7-47:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (62:5-62:48)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_alias (12:7-12:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq1_input_files (8:5-8:37)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: subsampled_metrics_interval_list (34:7-34:45)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq2_input_files (9:5-9:37)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (46:7-46:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: force_no_check (60:5-60:27)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (48:7-48:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ignore_r1_read_length (68:5-68:34)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: variant_rsids_file (33:7-33:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_ids (6:5-6:28)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (49:7-49:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_names (7:5-7:31)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: zcall_thresholds_file (29:7-29:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (63:5-63:30)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (22:12-22:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: paired_end (5:5-5:23)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:12-23:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r1_fastq (58:5-58:18)" +document = "broadinstitute/warp:verification/test-wdls/TestIlluminaGenotypingArray.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tenx_chemistry_version (65:5-65:31)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (108:1-108:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: whitelist_v2 (66:5-66:24)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (47:1-47:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CheckInputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: whitelist_v3 (67:5-67:24)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (73:1-73:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CreateCountMatrix.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (72:1-72:2)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (76:1-76:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CreateCountMatrix.wdl" -message = "[v1::W002::Style/Medium] curly command found (30:3-41:4)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (92:1-92:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CreateCountMatrix.wdl" -message = "[v1::W002::Style/Medium] curly command found (86:3-93:4)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W001::Style/Low] trailing space (112:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CreateCountMatrix.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: col_indices (63:5-63:28)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W001::Style/Low] trailing space (154:50)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/CreateCountMatrix.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: row_indices (62:5-62:28)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W001::Style/Low] trailing space (156:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/FastqToUBam.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (63:1-63:2)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W001::Style/Low] trailing space (158:52)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/FastqToUBam.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (72:1-72:2)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bcf_index_suffix (33:7-33:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/FastqToUBam.wdl" -message = "[v1::W002::Style/Medium] curly command found (34:3-62:4)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bcf_suffix (32:7-32:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/FeatureCounts.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: aligned_bam_inputs (6:5-6:35)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chunkLength (12:7-12:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/FeatureCounts.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotation_gtf (8:5-8:24)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chunkOverlaps (13:7-13:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/FeatureCounts.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_ids (7:5-7:28)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chunks_fail_threshold (29:7-29:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/GroupMetricsOutputs.wdl" -message = "[v1::W002::Style/Medium] curly command found (36:2-45:2)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contigs (22:7-22:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/GroupMetricsOutputs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_row_optional_outputs (6:5-6:44)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: frac_above_maf_5_percent_well_imputed_threshold (28:7-28:66)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W002::Style/Medium] curly command found (152:5-172:6)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genetic_maps_eagle (24:7-24:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: add_emptydrops_data (32:5-32:39)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (41:7-41:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotation_file (118:9-118:29)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: m3vcf_suffix (34:7-34:48)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotation_file (18:5-18:25)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: merge_ssvcf_mem_mb (27:7-27:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_id (126:9-126:21)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: multi_sample_vcf (14:7-14:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_id (26:5-26:17)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: multi_sample_vcf_index (15:7-15:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_id_exon (132:9-132:26)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: optional_qc_hwe (20:7-20:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_metrics (120:9-120:26)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: optional_qc_max_missing (19:7-19:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_metrics (20:5-20:22)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_callset_name (25:7-25:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counting_mode (31:5-31:36)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: perform_extra_qc_steps (18:7-18:45)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (141:9-141:20)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (21:7-21:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (40:5-40:16)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_panel_path (23:7-23:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpuPlatform (197:5-197:46)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (38:7-38:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (139:9-139:23)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: single_sample_vcf_indices (17:7-17:45)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (38:5-38:19)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: single_sample_vcfs (16:7-16:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (10:5-10:65)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: split_output_to_single_sample (26:7-26:52)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (110:9-110:69)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (37:7-37:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: empty_drops_result (30:5-30:29)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (39:7-39:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_id (128:9-128:21)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (40:7-40:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_id (28:5-28:17)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vcf_index_suffix (31:7-31:46)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_id_exon (134:9-134:26)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vcf_suffix (30:7-30:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_metrics (122:9-122:26)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (12:11-12:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_metrics (22:5-22:22)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (13:11-13:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id (112:9-112:24)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:14-34:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id (12:5-12:20)" +document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id_metadata_field (115:9-115:40)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (119:1-119:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id_metadata_field (15:5-15:36)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (122:1-122:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_name (114:9-114:27)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (152:1-152:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_name (14:5-14:23)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (70:1-70:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_name_metadata_field (116:9-116:42)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W001::Style/Low] trailing space (156:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_name_metadata_field (16:5-16:38)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W001::Style/Low] trailing space (202:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (140:9-140:35)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W001::Style/Low] trailing space (204:57)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (39:5-39:31)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W001::Style/Low] trailing space (206:54)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nthreads (196:5-196:21)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W001::Style/Low] trailing space (208:50)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (136:9-136:32)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: axiomPoly_resource_vcf (38:7-38:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (35:5-35:28)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: axiomPoly_resource_vcf_index (39:7-39:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sparse_count_matrix (124:9-124:33)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: callset_name (13:7-13:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sparse_count_matrix (24:5-24:29)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cross_check_fingerprints (56:7-56:46)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/H5adUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sparse_count_matrix_exon (130:9-130:38)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_resource_vcf (40:7-40:42)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/HISAT2.wdl" -message = "[v1::W002::Style/Medium] curly command found (167:3-245:4)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_resource_vcf_index (41:7-41:54)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/HISAT2.wdl" -message = "[v1::W002::Style/Medium] curly command found (297:3-340:4)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf (18:7-18:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/HISAT2.wdl" -message = "[v1::W002::Style/Medium] curly command found (387:3-392:4)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf_index (19:7-19:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/HISAT2.wdl" -message = "[v1::W002::Style/Medium] curly command found (39:3-111:4)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: eval_interval_list (29:7-29:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/HISAT2.wdl" -message = "[v1::W002::Style/Medium] curly command found (441:3-498:4)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: excess_het_threshold (42:7-42:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (184:1-184:6)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gather_vcfs (48:7-48:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W002::Style/Medium] curly command found (182:5-199:6)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gnarly_scatter_count (53:7-53:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W002::Style/Medium] curly command found (263:5-283:6)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (64:7-64:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W002::Style/Medium] curly command found (32:3-44:4)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database (28:7-28:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: add_emptydrops_data (87:5-87:39)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hapmap_resource_vcf (30:7-30:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: alignment_summary_metrics (305:9-305:46)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hapmap_resource_vcf_index (31:7-31:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotation_file (229:9-229:29)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: huge_disk (23:7-23:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotation_file (400:5-400:25)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: indel_recalibration_annotation_values (27:7-27:59)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotation_file (73:5-73:25)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: indel_recalibration_tranche_values (26:7-26:56)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotation_introns_added_gtf (314:9-314:42)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: large_disk (22:7-22:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: batch_id (164:9-164:24)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: medium_disk (21:7-21:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: batch_name (165:9-165:27)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: mills_resource_vcf (36:7-36:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bead_locations (394:5-394:24)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: mills_resource_vcf_index (37:7-37:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_id (237:9-237:21)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: omni_resource_vcf (32:7-32:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_id (397:5-397:17)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: omni_resource_vcf_index (33:7-33:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_id (81:5-81:17)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: one_thousand_genomes_resource_vcf (34:7-34:45)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_id_exon (243:9-243:26)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: one_thousand_genomes_resource_vcf_index (35:7-35:51)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_metrics (231:9-231:26)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (17:7-17:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_metrics (395:5-395:22)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (15:7-15:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_metrics (75:5-75:22)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (16:7-16:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counting_mode (86:5-86:36)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rename_gvcf_samples (51:7-51:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (175:9-175:20)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (61:7-61:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (21:5-21:16)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: run_vets (49:7-49:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (252:9-252:20)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_name_map (14:7-14:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (325:9-325:20)" 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(25:7-25:56)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup_metrics (306:9-306:34)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: snp_recalibration_tranche_values (24:7-24:54)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (173:9-173:23)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: snp_vqsr_downsampleFactor (46:7-46:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (19:5-19:19)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: snps_variant_recalibration_threshold (50:7-50:56)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (250:9-250:23)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: targets_interval_list (45:7-45:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (323:9-323:23)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: top_level_scatter_count (47:7-47:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (93:5-93:19)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (60:7-60:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (405:5-405:27)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unbounded_scatter_count_scale_factor (52:7-52:56)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (172:9-172:77)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unpadded_intervals_file (12:7-12:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (221:9-221:80)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (62:7-62:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (303:9-303:77)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: 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within task: docker (6:5-6:73)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vqsr_indel_filter_level (44:7-44:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: empty_drops_result (85:5-85:29)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vqsr_snp_filter_level (43:7-43:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: exons_counts (312:9-312:33)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:12-38:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gc_bias_summary_metrics (307:9-307:44)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (39:12-39:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_id (239:9-239:21)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (46:12-46:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_id (398:5-398:17)" +document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_id (83:5-83:17)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (31:1-31:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_id_exon (245:9-245:26)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (41:1-41:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_metrics (233:9-233:26)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (44:1-44:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_metrics (396:5-396:22)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (51:1-51:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_metrics (77:5-77:22)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (54:1-54:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id (12:5-12:20)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (64:1-64:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id (223:9-223:24)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W001::Style/Low] trailing space (68:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id (401:5-401:20)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W001::Style/Low] trailing space (88:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id (67:5-67:20)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: callset_name (17:7-17:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id_metadata_field (14:5-14:36)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (25:7-25:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id_metadata_field (226:9-226:40)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: preemptible_tries (18:7-18:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id_metadata_field (318:9-318:40)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (16:7-16:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id_metadata_field (70:5-70:36)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (14:7-14:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_ids (316:9-316:32)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (15:7-15:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_name (13:5-13:23)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (22:7-22:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_name (225:9-225:27)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_indices_fofn (13:7-13:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_name (69:5-69:23)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: samples_fofn (12:7-12:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_name_metadata_field (15:5-15:38)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (21:7-21:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_name_metadata_field (227:9-227:42)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (23:7-23:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_name_metadata_field (319:9-319:42)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (24:7-24:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_name_metadata_field (71:5-71:38)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_names (317:9-317:35)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (47:1-47:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: introns_counts (310:9-310:35)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (73:1-73:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: library (168:9-168:24)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (76:1-76:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: loom_input (163:9-163:31)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (85:1-85:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (174:9-174:34)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (88:1-88:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (20:5-20:31)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (98:1-98:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (251:9-251:35)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W001::Style/Low] trailing space (102:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (324:9-324:34)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W001::Style/Low] trailing space (127:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (94:5-94:31)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W001::Style/Low] trailing space (129:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_mb (406:5-406:26)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: batch_id (25:7-25:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: organ (170:9-170:22)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: batch_name (26:7-26:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (171:9-171:32)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq1_input_files (23:7-23:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (17:5-17:28)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq2_input_files (24:7-24:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (247:9-247:32)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gene_ref_flat (14:7-14:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (321:9-321:32)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genome_ref_fasta (12:7-12:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (402:5-402:28)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (41:7-41:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pipeline_version (90:5-90:28)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_index (17:7-17:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_id (166:9-166:27)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_name (15:7-15:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: project_name (167:9-167:29)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_trans_index (18:7-18:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rsem_gene_results (8:5-8:27)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_trans_name (16:7-16:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: smartseq_qc_files (10:5-10:34)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id_metadata_field (33:7-33:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sparse_count_matrix (235:9-235:33)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_ids (21:7-21:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sparse_count_matrix (399:5-399:29)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_name_metadata_field (32:7-32:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sparse_count_matrix (79:5-79:29)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_names (22:7-22:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sparse_count_matrix_exon (241:9-241:38)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: library (29:7-29:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/LoomUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: species (169:9-169:24)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: organ (31:7-31:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/MergeSortBam.wdl" -message = "[v1::W002::Style/Medium] curly command found (38:3-47:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: paired_end (34:7-34:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/MergeSortBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: compression_level (9:5-9:30)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: project_id (27:7-27:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/MergeSortBam.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_filename (7:5-7:31)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: project_name (28:7-28:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (31:1-31:2)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (38:7-38:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (34:1-34:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rrna_intervals (13:7-13:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (75:1-75:2)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rsem_ref_index (19:7-19:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (95:1-95:2)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: species (30:7-30:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W001::Style/Low] trailing space (138:36)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: stranded (20:7-20:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W001::Style/Low] trailing space (15:86)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (37:7-37:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W001::Style/Low] trailing space (246:43)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (39:7-39:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W001::Style/Low] trailing space (92:47)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (40:7-40:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W002::Style/Medium] curly command found (110:3-133:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (15:12-15:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W002::Style/Medium] curly command found (178:3-196:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (16:12-16:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W002::Style/Medium] curly command found (32:3-65:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (17:12-17:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (224:5-224:17)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (18:12-18:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (226:5-226:51)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:21-23:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (223:5-223:65)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (24:21-24:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id (85:5-85:20)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id (8:5-8:20)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (41:1-41:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mb (225:5-225:27)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (61:1-61:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Metrics.wdl" -message 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"broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" +message = "[v1::W001::Style/Low] trailing space (117:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/ModifyGtf.wdl" -message = "[v1::W002::Style/Medium] curly command found (30:3-44:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" +message = "[v1::W001::Style/Low] trailing space (90:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id (8:9-8:24)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: adapter_list (15:7-15:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Picard.wdl" -message = 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within workflow: batch_name (21:7-21:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Picard.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (277:1-277:2)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq1_input_files (18:7-18:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Picard.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (291:1-291:2)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq2_input_files (19:7-19:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Picard.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (323:1-323:2)" +document = 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: adapter_seq_read3 (44:7-44:69)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Picard.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (58:9-58:28)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: annotations_gtf (20:7-20:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Picard.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sort_order (49:9-49:41)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_r1_fastq (33:7-33:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/Picard.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sort_order (6:9-6:41)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_r2_fastq (34:7-34:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RSEM.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (18:1-18:2)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_r3_fastq (35:7-35:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RSEM.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (36:1-36:2)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_whitelist (46:7-46:95)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RSEM.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (9:1-9:2)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chrom_sizes (41:7-41:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RSEM.wdl" -message = "[v1::W002::Style/Medium] curly command found (34:3-48:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: count_exons (27:7-27:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RSEM.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: is_paired (8:5-8:22)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: counting_mode (15:7-15:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RunEmptyDrops.wdl" -message = "[v1::W002::Style/Medium] curly command found (40:5-48:6)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: emptydrops_lower (23:7-23:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RunEmptyDrops.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size (23:9-23:34)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: force_no_check (24:7-24:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RunEmptyDrops.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (19:9-19:74)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gex_i1_fastq (18:7-18:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RunEmptyDrops.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: emptydrops_lower (16:9-16:35)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gex_r1_fastq (16:7-16:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RunEmptyDrops.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fdr_cutoff (12:9-12:32)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gex_r2_fastq (17:7-17:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RunEmptyDrops.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (20:9-20:35)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gex_whitelist (28:7-28:93)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RunEmptyDrops.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_molecules (15:9-15:32)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (53:7-53:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/RunEmptyDrops.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: niters (11:9-11:31)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ignore_r1_read_length (25:7-25:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/SplitBamByCellBarcode.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (44:1-44:2)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id (12:7-12:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/SplitBamByCellBarcode.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (53:1-53:2)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: mt_genes (21:7-21:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/SplitBamByCellBarcode.wdl" -message = "[v1::W002::Style/Medium] curly command found (34:3-43:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (50:7-50:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (436:1-436:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: run_cellbender (54:7-54:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (473:1-473:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: soloMultiMappers (29:7-29:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (479:1-479:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: star_strand_mode (26:7-26:42)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (485:1-485:1)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tar_bwa_reference (38:7-38:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (497:1-497:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tar_star_reference (19:7-19:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W001::Style/Low] trailing space (643:44)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tenx_chemistry_version (22:7-22:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W002::Style/Medium] curly command found (100:3-118:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (49:7-49:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W002::Style/Medium] curly command found (32:3-52:4)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (51:7-51:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: align_features (434:5-434:32)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (52:7-52:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: barcodes (429:5-429:25)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (16:19-16:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cell_reads (432:5-432:28)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (17:19-17:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chemistry (221:5-221:18)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (18:20-18:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_exons (225:5-225:25)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:15-25:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_exons (538:5-538:25)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:15-29:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counting_mode (223:5-223:25)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:19-33:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (543:5-543:16)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:19-34:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (545:5-545:127)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:19-35:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk (650:5-650:18)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (43:14-43:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker (541:5-541:78)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (44:14-44:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: features (430:5-430:25)" +document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_id (437:5-437:20)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (11:1-11:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: machine_mem_mb (542:5-542:31)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (39:1-39:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: matrix (431:5-431:23)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (46:1-46:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (224:5-224:31)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W001::Style/Low] trailing space (53:96)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_bam_basename (536:5-536:31)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W001::Style/Low] trailing space (91:49)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preemptible (547:5-547:24)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: annotations_gtf (26:5-26:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r1_fastq (532:5-532:25)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: count_exons (48:5-48:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: r2_fastq (533:5-533:25)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: counting_mode (13:5-13:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_structure (537:5-537:26)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: emptydrops_lower (35:5-35:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: summary (433:5-433:25)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: force_no_check (38:5-38:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tar_star_reference (534:5-534:28)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (60:5-60:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: umipercell (435:5-435:28)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: i1_fastq (18:5-18:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: white_list (220:5-220:20)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ignore_r1_read_length (42:5-42:42)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/StarAlign.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: whitelist (535:5-535:19)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id (19:5-19:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/TrimAdapters.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: adapter_list (8:5-8:22)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id_metadata_field (22:5-22:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/TrimAdapters.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq1_input_files (6:5-6:35)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_name (21:5-21:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/TrimAdapters.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastq2_input_files (7:5-7:35)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_name_metadata_field (23:5-23:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/TrimAdapters.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_ids (9:5-9:28)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: mt_genes (27:5-27:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/accessory_workflows/build_bwa_reference/bwa-mk-index.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: chrom_sizes_file (26:9-26:30)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_bam_basename (20:5-20:42)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/accessory_workflows/build_bwa_reference/bwa-mk-index.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_name (24:9-24:24)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r1_fastq (16:5-16:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/accessory_workflows/build_bwa_reference/bwa-mk-index.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_fasta (25:9-25:29)" +document = "broadinstitute/warp:verification/test-wdls/TestOptimus.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r2_fastq (17:5-17:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tasks/skylab/accessory_workflows/build_bwa_reference/bwa-mk-index.wdl" -message = "[v1::W003::Completeness/Medium] missing 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meta within workflow: truth_bam (13:5-13:26)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bead_locations (21:7-21:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tests/skylab/smartseq2_single_nucleus/pr/test_smartseq2_single_nucleus_PR.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_exon_intron_counts_hash (12:5-12:48)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: count_exons (20:7-20:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:tests/skylab/smartseq2_single_nucleus/pr/test_smartseq2_single_nucleus_PR.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_loom (14:5-14:20)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (28:7-28:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bead_pool_manifest_file (29:5-29:33)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: i1_fastq (14:7-14:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (46:5-46:18)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id (15:7-15:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_fp_vcf (35:5-35:21)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_bam_basename (19:7-19:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_green_idat_md5 (41:5-41:29)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r1_fastq (12:7-12:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gtc (27:5-27:18)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r2_fastq (13:7-13:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (25:5-25:29)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read_structure (16:7-16:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_params_file (44:5-44:26)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (25:7-25:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_red_idat_md5 (38:5-38:27)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tar_star_reference (17:7-17:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_vcf (32:5-32:18)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (24:7-24:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_fp_vcf (34:5-34:22)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (26:7-26:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_green_idat_md5 (40:5-40:30)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (27:7-27:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gtc (28:5-28:19)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (12:19-12:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (24:5-24:30)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (13:19-13:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_params_file (43:5-43:27)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (14:20-14:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_red_idat_md5 (37:5-37:28)" +document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf (31:5-31:19)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (102:1-102:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (31:5-31:18)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (41:1-41:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_fingerprint_vcf (28:5-28:30)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (61:1-61:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (25:5-25:30)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (64:1-64:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_fingerprint_vcf (29:5-29:31)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (77:1-77:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (26:5-26:31)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (80:1-80:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCramToUnmappedBams.wdl" -message = "[v1::W002::Style/Medium] curly command found (38:3-43:4)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (91:1-91:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_bam (31:5-31:18)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W001::Style/Low] trailing space (106:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_bam (32:5-32:19)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W001::Style/Low] trailing space (143:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bam_pairs (7:5-7:29)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W001::Style/Low] trailing space (145:68)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" -message = "[v1::W002::Style/Medium] curly command found (35:3-40:4)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W001::Style/Low] trailing space (147:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_bam (28:5-28:18)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W001::Style/Low] trailing space (149:50)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_bam (29:5-29:19)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq1 (26:7-26:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (9:5-9:18)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq2 (27:7-27:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_bam (8:5-8:25)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gene_ref_flat (14:7-14:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyCramToUnmappedBamsUpdated.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_bam (7:5-7:26)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genome_ref_fasta (12:7-12:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W002::Style/Medium] curly command found (69:3-74:4)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (35:7-35:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_bam (62:5-62:18)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_index (15:7-15:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_bam (63:5-63:19)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_name (18:7-18:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (24:5-24:18)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_trans_index (16:7-16:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_bams (21:5-21:26)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_trans_name (19:7-19:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_crai (14:5-14:19)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id (21:7-21:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_cram (13:5-13:19)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id_metadata_field (23:7-23:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gvcf (18:5-18:19)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_name (22:7-22:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gvcf_index (19:5-19:25)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_name_metadata_field (24:7-24:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (9:5-9:29)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_name (25:7-25:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_bams (22:5-22:27)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: paired_end (28:7-28:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_crai (12:5-12:20)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (32:7-32:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_cram (11:5-11:20)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rrna_intervals (13:7-13:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gvcf (16:5-16:20)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rsem_ref_index (17:7-17:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gvcf_index (17:5-17:26)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: stranded (20:7-20:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (8:5-8:30)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (31:7-31:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" -message = "[v1::W001::Style/Low] trailing space (26:31)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (33:7-33:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" -message = "[v1::W002::Style/Medium] curly command found (24:5-32:6)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (34:7-34:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: destination_cloud_path (21:9-21:38)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (15:12-15:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: done (20:9-20:21)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (16:12-16:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: destination_cloud_path (7:9-7:38)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (18:14-18:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyExternalReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (6:9-6:21)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (19:14-19:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyGDCSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (17:5-17:18)" +document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:12-26:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyGDCSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_bai (15:5-15:18)" +document = 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"broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (48:7-48:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyIlluminaGenotypingArray.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf (31:5-31:19)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (49:7-49:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: basename (139:5-139:20)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: firstInputIndices (137:5-137:34)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (33:1-33:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: firstInputs (135:5-135:28)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (45:1-45:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: haplotypeDatabase (140:5-140:125)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (48:1-48:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: picard_docker (141:5-141:76)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (63:1-63:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: secondInputIndices (138:5-138:35)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (66:1-66:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: secondInputs (136:5-136:29)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (79:1-79:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_metrics (112:5-112:22)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (90:1-90:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_metrics (113:5-113:23)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W001::Style/Low] trailing space (132:50)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (43:5-43:18)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W001::Style/Low] trailing space (134:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_multi_sample_vcf (35:5-35:33)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W001::Style/Low] trailing space (136:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_multi_sample_vcf_index (36:5-36:39)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W001::Style/Low] trailing space (94:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_single_sample_vcfs (37:5-37:42)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: alignment_references (13:7-13:47)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_single_sample_vcfs_indices (38:5-38:50)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (17:7-17:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_callset_name (25:5-25:31)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_sites (12:7-12:45)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: single_sample_test_vcf (41:5-41:40)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (27:7-27:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: single_sample_truth_vcf (40:5-40:41)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam_list (16:7-16:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: split_output_to_single_sample (24:5-24:42)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram_list (15:7-15:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (28:5-28:29)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reads_per_split (19:7-19:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_vcf (31:5-31:18)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (24:7-24:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_vcf_index (32:5-32:24)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rsq_threshold (18:7-18:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (27:5-27:30)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: save_bam_file (20:7-20:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf (30:5-30:19)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (23:7-23:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf_index (33:5-33:25)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (25:7-25:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (78:1-78:2)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (26:7-26:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W002::Style/Medium] curly command found (90:3-93:4)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vcf_post_processing (14:7-14:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_fingerprint (86:5-86:26)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:47)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_fingerprint (87:5-87:27)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (102:1-102:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (25:5-25:18)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (36:1-36:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_fingerprint (22:5-22:27)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (51:1-51:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_intervals (16:5-16:31)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (54:1-54:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (19:5-19:29)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (75:1-75:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_vcf_indexes (12:5-12:33)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (78:1-78:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_vcfs (11:5-11:26)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (91:1-91:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_fingerprint (23:5-23:28)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] trailing space (106:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_intervals (17:5-17:32)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] trailing space (155:50)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (20:5-20:30)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] trailing space (157:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf_indexes (14:5-14:34)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] trailing space (159:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcfs (13:5-13:27)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] trailing space (161:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W002::Style/Medium] curly command found (52:3-58:4)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] trailing space (163:58)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dependency_input (73:5-73:27)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W001::Style/Low] trailing space (165:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: error_msg (49:5-49:41)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: alignment_references (13:7-13:47)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: extra_args (78:5-78:34)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (18:7-18:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file1 (74:5-74:15)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_sites (12:7-12:45)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file2 (75:5-75:15)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: filtering_model_no_gt_name (23:7-23:78)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_to_ignore (77:5-77:41)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (30:7-30:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: num1 (47:5-47:13)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam_list (17:7-17:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: num2 (48:5-48:13)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram_list (16:7-16:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_file (76:5-76:23)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: make_haplotype_bam (21:7-21:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: report_files (105:5-105:29)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: merge_bam_file (20:7-20:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (6:5-6:29)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reads_per_split (22:7-22:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMetrics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (7:5-7:30)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (27:7-27:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (25:5-25:18)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rsq_threshold (19:7-19:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_vcf (24:5-24:18)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (26:7-26:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf (23:5-23:19)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (28:7-28:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMultiSampleSmartSeq2.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (23:1-23:2)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: variant_calling_settings (14:7-14:54)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (12:5-12:18)" +document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gene_metrics (14:5-14:27)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (76:1-76:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyOptimus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_h5ad (8:5-8:19)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (86:1-86:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyOptimus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_bam (12:5-12:19)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (89:1-89:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyOptimus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_cell_metrics (18:5-18:28)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (96:1-96:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyOptimus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gene_metrics (15:5-15:28)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W001::Style/Low] trailing space (111:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyOptimus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_h5ad (9:5-9:20)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W001::Style/Low] trailing space (136:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (125:5-125:13)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W001::Style/Low] trailing space (138:54)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: comparison (187:5-187:20)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: agg_preemptible_tries (29:7-29:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_bam (151:5-151:18)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (27:7-27:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: tolerance (188:5-188:20)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: break_bands_at_multiples_of (17:7-17:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_bam (152:5-152:19)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: calling_interval_list (14:7-14:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: compare_transcriptome_dup_metrics (26:5-26:46)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination (18:7-18:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (28:5-28:18)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf (25:7-25:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_exon_counts (21:5-21:26)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf_index (26:7-26:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gene_counts (19:5-19:26)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: evaluation_interval_list (15:7-15:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gene_tpm (17:5-17:23)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: final_vcf_base_name (28:7-28:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (9:5-9:29)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (41:7-41:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_output_bam (13:5-13:25)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_scatter_count (16:7-16:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_text_metrics (11:5-11:34)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (19:7-19:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_transcriptome_bam (15:5-15:32)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam_index (20:7-20:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_transcriptome_duplicate_metrics (23:5-23:46)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: make_bamout (31:7-31:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: transcriptome_deterministic (25:5-25:40)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: make_gvcf (30:7-30:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_exon_counts (22:5-22:27)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (23:7-23:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gene_counts (20:5-20:27)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (21:7-21:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gene_tpm (18:5-18:24)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (22:7-22:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (10:5-10:30)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_str (24:7-24:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_output_bam (14:5-14:26)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (38:7-38:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_text_metrics (12:5-12:35)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: run_dragen_mode_variant_calling (12:7-12:54)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_transcriptome_bam (16:5-16:33)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: skip_reblocking (33:7-33:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyRNAWithUMIs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_transcriptome_duplicate_metrics (24:5-24:47)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (37:7-37:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W002::Style/Medium] curly command found (66:3-71:4)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (39:7-39:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_bam (59:5-59:18)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_dragen_hard_filtering (34:7-34:48)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_bam (60:5-60:19)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_gatk3_haplotype_caller (32:7-32:49)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bam_pairs (8:5-8:29)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_spanning_event_genotyping (13:7-13:51)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_crai (16:5-16:19)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (40:7-40:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_cram (15:5-15:19)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:15-32:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gvcf (20:5-20:19)" +document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gvcf_index (21:5-21:25)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: allow_empty_ref_alt (33:5-33:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (11:5-11:29)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dragen_functional_equivalence_mode (25:5-25:55)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_crai (14:5-14:20)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dragen_maximum_quality_mode (26:5-26:48)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_cram (13:5-13:20)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dragmap_reference (13:5-13:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gvcf (18:5-18:20)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_file (17:5-17:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gvcf_index (19:5-19:26)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_index (18:5-18:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (10:5-10:30)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (41:5-41:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (23:5-23:18)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: papi_settings (15:5-15:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_bam (11:5-11:18)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: perform_bqsr (31:5-31:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_cell_metrics (17:5-17:27)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: provide_bam_output (22:5-22:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gene_metrics (14:5-14:27)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: references (12:5-12:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_loom (8:5-8:19)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (38:5-38:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_umi_metrics (20:5-20:26)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: run_dragen_mode_variant_calling (28:5-28:52)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_bam (12:5-12:19)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_and_unmapped_bams (11:5-11:51)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_cell_metrics (18:5-18:28)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: scatter_settings (14:5-14:51)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gene_metrics (15:5-15:28)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (37:5-37:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_loom (9:5-9:20)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unmap_contaminant_reads (30:5-30:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_umi_metrics (21:5-21:27)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (39:5-39:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (18:5-18:18)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_bwa_mem (32:5-32:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_bam (10:5-10:18)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_dragen_hard_filtering (34:5-34:46)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_loom (14:5-14:19)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_gatk3_haplotype_caller (23:5-23:46)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (16:5-16:29)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_spanning_event_genotyping (29:5-29:49)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_transcriptome_bam (12:5-12:32)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (40:5-40:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_bam (9:5-9:19)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: wgs_coverage_interval_list (20:5-20:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_loom (13:5-13:20)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:13-23:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (15:5-15:30)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (8:10-8:45)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_transcriptome_bam (11:5-11:33)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (121:1-121:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_crai (15:5-15:19)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (132:1-132:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_cram (14:5-14:19)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (39:1-39:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (10:5-10:29)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (57:1-57:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_crai (13:5-13:20)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (60:1-60:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_cram (12:5-12:20)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (86:1-86:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifySomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (9:5-9:30)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (89:1-89:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (64:1-64:2)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] trailing space (136:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W002::Style/Medium] curly command found (76:3-79:4)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] trailing space (185:50)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_fingerprint (72:5-72:26)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] trailing space (187:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_fingerprint (73:5-73:27)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] trailing space (189:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (25:5-25:18)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] trailing space (191:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_fingerprint (22:5-22:26)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] trailing space (193:54)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_intervals (16:5-16:31)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W001::Style/Low] trailing space (195:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (19:5-19:29)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (16:7-16:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_vcf_indexes (12:5-12:33)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta (19:7-19:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_vcfs (11:5-11:26)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta_index (20:7-20:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_fingerprint (23:5-23:27)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: final_gvcf_base_name (17:7-17:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_intervals (17:5-17:32)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_file (24:7-24:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (20:5-20:30)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_index (25:7-25:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf_indexes (14:5-14:34)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (33:7-33:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcfs (13:5-13:27)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (13:7-13:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dependency_input (89:5-89:27)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram (12:7-12:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file1 (90:5-90:15)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_map (14:7-14:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file2 (91:5-91:15)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: papi_settings (23:7-23:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_to_ignore (93:5-93:36)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: references (21:7-21:46)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_file (92:5-92:23)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (30:7-30:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (17:5-17:18)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_name (15:7-15:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_crai (14:5-14:19)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: scatter_settings (22:7-22:53)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_cram (12:5-12:19)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (29:7-29:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_metrics (9:5-9:29)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unmapped_bam_suffix (18:7-18:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_crai (15:5-15:20)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (31:7-31:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_cram (13:5-13:20)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (32:7-32:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_metrics (10:5-10:30)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: wgs_coverage_interval_list (26:7-26:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (143:1-143:2)" +document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W002::Style/Medium] curly command found (122:3-135:4)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (31:1-31:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dependency_input (148:5-148:27)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (41:1-41:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file1 (149:5-149:15)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (44:1-44:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file2 (150:5-150:15)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (57:1-57:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: metrics_to_ignore (152:5-152:36)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (69:1-69:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_file (151:5-151:23)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (79:1-79:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: test_gvcf (117:5-117:19)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W001::Style/Low] trailing space (108:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: truth_gvcf (118:5-118:20)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W001::Style/Low] trailing space (110:59)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (25:5-25:18)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W001::Style/Low] trailing space (83:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_crai (14:5-14:19)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bin_size_list (18:7-18:37)" [[concerns]] kind = "LintWarning" -document = 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parameter meta within workflow: input_id (14:7-14:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_crai (15:5-15:20)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_reference (16:7-16:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_cram (13:5-13:20)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_bam (17:7-17:52)" [[concerns]] kind = "LintWarning" -document = 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workflow: truth_metrics (10:5-10:30)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (23:7-23:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf (18:5-18:19)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (24:7-24:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bead_pool_manifest_file (26:5-26:33)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (12:12-12:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (40:5-40:18)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (13:12-13:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_genotype_concordance_vcf (31:5-31:39)" +document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_gtc (24:5-24:18)" +document = 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_vcf (28:5-28:18)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (61:1-61:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_genotype_concordance_vcf (32:5-32:40)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (64:1-64:4)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_gtc (25:5-25:19)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (74:1-74:2)" [[concerns]] 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: chromosome_sizes (20:7-20:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyscATAC.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (11:1-11:4)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_input_read1 (12:7-12:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (12:5-12:18)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_input_read2 (13:7-13:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_bam (8:5-8:18)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genome_fa (21:7-21:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: test_matrix_files (10:5-10:34)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (28:7-28:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_bam (7:5-7:19)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: mapping_yaml (18:7-18:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifyscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_matrix_files (9:5-9:35)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_basename (16:7-16:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifysnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: done (11:9-11:22)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: plate_id (15:7-15:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/VerifysnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: 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= "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (20:1-20:2)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tarred_index_files (17:7-17:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (237:1-237:2)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (24:7-24:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (23:1-23:2)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (26:7-26:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (244:1-244:2)" +document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (27:7-27:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (29:1-29:2)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (45:1-45:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (32:1-32:2)" +document = 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"broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chromosome_sizes (18:7-18:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (58:1-58:2)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: compress_level (29:7-29:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (66:1-66:2)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker (39:7-39:68)" [[concerns]] kind = "LintWarning" -document = 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parameter meta within workflow: genome_fa (17:7-17:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (82:1-82:2)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (37:7-37:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (85:1-85:2)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (26:7-26:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (90:1-90:2)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: num_downstr_bases (28:7-28:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (93:1-93:4)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: num_upstr_bases (27:7-27:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] trailing space (213:15)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: plate_id (15:7-15:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] trailing space (245:65)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r1_adapter (19:7-19:54)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] trailing space (252:57)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r1_left_cut (22:7-22:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] trailing space (259:59)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r1_right_cut (23:7-23:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W001::Style/Low] trailing space (266:56)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r2_adapter (20:7-20:54)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: analysis_version_number (12:7-12:35)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r2_left_cut (24:7-24:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: arrays_control_data_path (84:7-84:39)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r2_right_cut (25:7-25:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: arrays_metadata_path (43:7-43:35)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: random_primer_indexes (14:7-14:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bead_pool_manifest_file (46:7-46:36)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (34:7-34:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bead_pool_manifest_filename (45:7-45:42)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tarred_index_files (16:7-16:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: call_rate_threshold (21:7-21:39)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (33:7-33:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chip_well_barcode (11:7-11:31)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (35:7-35:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cluster_file (49:7-49:25)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (36:7-36:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cluster_filename (48:7-48:31)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (12:19-12:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: collaborator_participant_id (18:7-18:42)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (13:19-13:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_controls_vcf (78:7-78:39)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (19:14-19:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: control_sample_intervals_file (89:7-89:42)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (20:14-20:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: control_sample_name (86:7-86:34)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (22:11-22:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: control_sample_vcf_file (87:7-87:36)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:11-23:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: control_sample_vcf_index_file (88:7-88:42)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (24:11-24:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbSNP_vcf (30:7-30:21)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:11-25:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbSNP_vcf_index (31:7-31:27)" +document = "broadinstitute/warp:verification/test-wdls/Testsnm3C.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: disk_size (91:7-91:20)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (274:1-274:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: environment (101:7-101:25)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (279:1-279:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: extended_chip_manifest_file (57:7-57:40)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (280:1-280:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_vcf_file (63:7-63:43)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (285:1-285:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_vcf_index_file (64:7-64:49)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (317:1-317:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gender_cluster_file (52:7-52:32)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (322:1-322:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gender_cluster_filename (51:7-51:38)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (323:1-323:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genotype_concordance_threshold (22:7-22:50)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (326:1-326:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (100:7-100:39)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (328:1-328:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: green_idat_cloud_path (25:7-25:33)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (331:1-331:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database_file (65:7-65:35)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (358:1-358:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lab_batch (34:7-34:24)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (363:1-363:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minor_allele_frequency_file (81:7-81:40)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (395:1-395:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: params_file (33:7-33:24)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (400:1-400:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: participant_id (19:7-19:29)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (406:1-406:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: preemptible_tries (92:7-92:28)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (411:1-411:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: product_family (35:7-35:29)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (414:1-414:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: product_name (36:7-36:27)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (416:1-416:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: product_order_id (37:7-37:31)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (419:1-419:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: product_part_number (38:7-38:34)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (424:1-424:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: product_type (39:7-39:31)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (427:1-427:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read_fingerprint_from_mercury (62:7-62:52)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (429:1-429:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: red_idat_cloud_path (24:7-24:31)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (432:1-432:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (28:7-28:20)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (434:1-434:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (26:7-26:21)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (435:1-435:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (27:7-27:27)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (438:1-438:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: regulatory_designation (40:7-40:37)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (440:1-440:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reported_gender (17:7-17:29)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (441:1-441:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: research_project_id (41:7-41:34)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (443:1-443:12)" [[concerns]] kind = "LintWarning" -document = 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(529:9-529:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_sites (18:7-18:45)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: card_json (557:9-557:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: environment (39:7-39:25)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: card_json (561:9-561:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: filtering_model_no_gt_name (29:7-29:78)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: card_json (583:9-583:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (38:7-38:39)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: card_json (587:9-587:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database_file (14:7-14:133)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: card_ontology (246:9-246:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam_list (23:7-23:34)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: card_ontology (251:9-251:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram_list (22:7-22:35)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_sizes (183:9-183:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: make_haplotype_bam (27:7-27:41)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: clusters (182:9-182:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: merge_bam_file (26:7-26:36)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fa (556:9-556:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_basename (13:7-13:29)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fa (560:9-560:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reads_per_split (28:7-28:37)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fa (647:9-647:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (34:7-34:26)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fa (652:9-652:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rsq_threshold (25:7-25:32)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fa (755:9-755:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_lsid (12:7-12:25)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fa (760:9-760:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tdr_dataset_uuid (16:7-16:31)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (184:9-184:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (33:7-33:24)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (247:9-247:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (35:7-35:27)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (252:9-252:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: variant_calling_settings (20:7-20:54)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (497:9-497:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (36:7-36:30)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (502:9-502:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path_arrays (37:7-37:37)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (529:9-529:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestBroadInternalUltimaGenomics.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vcf_post_processing (21:7-21:44)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (534:9-534:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (41:1-41:2)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (558:9-558:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (63:1-63:4)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (562:9-562:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (69:1-69:36)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (584:9-584:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (72:1-72:4)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (588:9-588:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (78:1-78:36)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (612:9-612:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (89:1-89:2)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (616:9-616:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W001::Style/Low] trailing space (118:50)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (652:9-652:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W001::Style/Low] trailing space (120:64)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (657:9-657:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W001::Style/Low] trailing space (93:15)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (697:9-697:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: environment (34:7-34:25)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (702:9-702:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_vcf (18:7-18:38)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (757:9-757:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_vcf_index (19:7-19:44)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (762:9-762:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (35:7-35:39)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: final_summary (756:9-756:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database_file (26:7-26:35)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: final_summary (761:9-761:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (14:7-14:22)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_coverage (245:9-245:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam_index (15:7-15:28)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_coverage (250:9-250:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_sample_alias (16:7-16:33)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filtered_reads (180:9-180:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_vcf (12:7-12:22)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: intermediate_files (651:9-651:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_vcf_index (13:7-13:28)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: intermediate_files (656:9-656:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_basename (22:7-22:29)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kma_output (243:9-243:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read_fingerprint_from_mercury (17:7-17:52)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kma_output (248:9-248:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (25:7-25:20)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kma_species_output (244:9-244:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (23:7-23:21)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kma_species_output (249:9-249:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (24:7-24:27)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kmer_db (493:9-493:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (30:7-30:26)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kmer_db (498:9-498:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_alias (21:7-21:26)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kmer_db (525:9-525:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_lsid (20:7-20:26)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kmer_db (530:9-530:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (29:7-29:24)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_amr_results (695:9-695:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (31:7-31:27)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_amr_results (700:9-700:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (32:7-32:30)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_output (241:9-241:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCheckFingerprint.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path_arrays (33:7-33:38)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_output (246:9-246:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (32:1-32:2)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_output_json (491:9-491:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (43:1-43:2)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_output_json (496:9-496:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (46:1-46:4)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_output_json (696:9-696:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (52:1-52:36)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_output_json (701:9-701:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (55:1-55:4)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_reports (649:9-649:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (65:1-65:2)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_reports (654:9-654:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (93:1-93:2)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_species_output (242:9-242:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W001::Style/Low] trailing space (69:15)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_species_output (247:9-247:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W001::Style/Low] trailing space (89:42)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_contig_length (611:9-611:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: additional_disk (19:7-19:31)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_contig_length (615:9-615:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (17:7-17:28)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: non_host_reads_fa (582:9-582:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (26:7-26:39)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: non_host_reads_fa (586:9-586:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (13:7-13:22)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: non_host_reads_fa (648:9-648:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram (12:7-12:23)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: non_host_reads_fa (653:9-653:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_map (16:7-16:23)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_sorted_length_100 (523:9-523:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (14:7-14:22)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_sorted_length_100 (528:9-528:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (15:7-15:28)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: raw_reports (650:9-650:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (23:7-23:26)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: raw_reports (655:9-655:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (22:7-22:24)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reduplicated_reads (610:9-610:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unmapped_bam_suffix (18:7-18:51)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reduplicated_reads (614:9-614:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (24:7-24:27)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_name (248:9-248:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestCramToUnmappedBams.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (25:7-25:30)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_name (253:9-253:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (165:1-165:4)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: subsampled_reads (181:9-181:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bait_interval_list (20:5-20:28)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wildcard_data (495:9-495:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bait_set_name (21:5-21:25)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wildcard_data (500:9-500:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_file (16:5-16:37)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wildcard_data (527:9-527:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_index (17:5-17:38)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wildcard_data (532:9-532:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (30:5-30:37)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wildcard_index (496:9-496:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: papi_settings (11:5-11:31)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wildcard_index (501:9-501:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: provide_bam_output (23:5-23:39)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wildcard_index (528:9-528:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: references (13:5-13:44)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wildcard_index (533:9-533:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (27:5-27:24)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: amr_kmer_db (28:9-28:92)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_and_unmapped_bams (12:5-12:51)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: card_json (25:9-25:81)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: scatter_settings (14:5-14:51)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: card_ontology (26:9-26:97)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: target_interval_list (19:5-19:30)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (22:9-22:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (26:5-26:22)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: filtered_sample (21:9-21:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (28:5-28:25)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filtering_docker_image_id (24:9-24:71)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (29:5-29:28)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: kmer_db (27:9-27:85)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bait_interval_list (34:5-34:28)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_contig_length (31:9-31:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bait_set_name (35:5-35:25)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: raw_sample (20:9-20:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (18:5-18:26)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (33:9-33:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta (24:5-24:25)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_name (23:9-23:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta_index (25:5-25:31)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: wildcard_data (29:9-29:106)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: final_gvcf_base_name (20:5-20:32)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: wildcard_index (30:9-30:106)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_file (31:5-31:37)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (178:6-178:14)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_index (32:5-32:38)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (244:6-244:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (42:5-42:37)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:16-33:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (14:5-14:20)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (494:6-494:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram (13:5-13:21)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (526:6-526:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_map (15:5-15:21)" +document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (558:6-558:16)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: papi_settings 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space (115:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalExomeReprocessing.wdl" -message = "[v1::W001::Style/Low] trailing space (133:15)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W001::Style/Low] trailing space (116:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalExomeReprocessing.wdl" -message = "[v1::W001::Style/Low] trailing space (144:98)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W001::Style/Low] trailing space (11:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalExomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bait_interval_list (20:7-20:30)" +document = 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"chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (189:9-189:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta (19:7-19:26)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ground_truth_nr (187:9-187:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta_index (20:7-20:32)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ground_truth_nt (186:9-186:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: destination_cloud_path (28:7-28:36)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_nr (183:9-183:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: final_gvcf_base_name (17:7-17:34)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_nt (182:9-182:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_file (22:7-22:39)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_ref_nr (185:9-185:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_index (23:7-23:40)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_ref_nt (184:9-184:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (35:7-35:39)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: step_counts (188:9-188:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (13:7-13:22)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxadb_sqlite (144:9-144:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram (12:7-12:23)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_counts (141:9-141:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_map (14:7-14:23)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_fasta_run_1 (9:9-9:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: papi_settings (26:7-26:33)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_fasta_run_2 (15:9-15:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: references (24:7-24:46)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_summary_run_1 (8:9-8:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (32:7-32:26)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_summary_run_2 (14:9-14:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_name (15:7-15:25)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (24:9-24:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: scatter_settings (25:7-25:53)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ground_truth (22:9-22:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (31:7-31:24)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: step_counts_run_1 (11:9-11:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unmapped_bam_suffix (18:7-18:33)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: step_counts_run_2 (17:9-17:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (33:7-33:27)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_counts_run_1 (7:9-7:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (34:7-34:30)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_counts_run_2 (13:9-13:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestExternalWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: wgs_coverage_interval_list (21:7-21:38)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W001::Style/Low] trailing space (12:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (102:1-102:2)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W001::Style/Low] trailing space (48:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (44:1-44:2)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W001::Style/Low] trailing space (66:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (90:1-90:4)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W001::Style/Low] trailing space (71:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (92:1-92:4)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W001::Style/Low] trailing space (82:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W001::Style/Low] trailing space (106:15)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W001::Style/Low] trailing space (96:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W001::Style/Low] trailing space (137:50)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbtype (70:9-70:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W001::Style/Low] trailing space (139:41)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (35:9-35:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W001::Style/Low] trailing space (141:41)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (50:9-50:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W001::Style/Low] trailing space (49:41)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (6:9-6:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (18:7-18:28)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (71:9-71:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_vcf (20:7-20:29)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ground_truth (69:9-69:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_vcf_index (21:7-21:35)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa (68:9-68:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta (14:7-14:27)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sc (34:9-34:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta_index (15:7-15:33)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: step_counts (5:9-5:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf (22:7-22:21)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W001::Style/Low] trailing space (13:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf_index (23:7-23:27)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W001::Style/Low] trailing space (23:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (38:7-38:39)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W001::Style/Low] trailing space (27:45)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (13:7-13:22)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W001::Style/Low] trailing space (28:87)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram (12:7-12:23)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W001::Style/Low] trailing space (29:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_map (16:7-16:23)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W001::Style/Low] trailing space (30:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_amb (27:7-27:19)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W001::Style/Low] trailing space (40:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_ann (28:7-28:19)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W001::Style/Low] trailing space (43:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_bwt (29:7-29:19)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W001::Style/Low] trailing space (44:87)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (26:7-26:20)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W001::Style/Low] trailing space (45:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fai (25:7-25:19)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W001::Style/Low] trailing space (46:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (24:7-24:21)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W001::Style/Low] trailing space (56:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_pac (30:7-30:19)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_fasta_run_1 (11:9-11:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_sa (31:7-31:18)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_fasta_run_2 (17:9-17:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestGDCWholeGenomeSomaticSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (35:7-35:26)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_summary_run_1 (10:9-10:35)" [[concerns]] kind = "LintWarning" -document = 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"[v1::W001::Style/Low] line contains only whitespace (47:1-47:2)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_ref_nt (186:9-186:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (73:1-73:2)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: step_counts (190:9-190:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (76:1-76:4)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxadb_sqlite (147:9-147:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (92:1-92:4)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_counts (144:9-144:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W001::Style/Low] trailing space (112:15)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_fasta_run_1 (10:9-10:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W001::Style/Low] trailing space (154:50)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_fasta_run_2 (16:9-16:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W001::Style/Low] trailing space (156:41)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_summary_run_1 (9:9-9:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W001::Style/Low] trailing space (158:52)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_summary_run_2 (15:9-15:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bcf_index_suffix (33:7-33:44)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (25:9-25:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bcf_suffix (32:7-32:33)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ground_truth (23:9-23:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chunkLength (12:7-12:33)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: step_counts_run_1 (12:9-12:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chunkOverlaps (13:7-13:34)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: step_counts_run_2 (18:9-18:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chunks_fail_threshold (29:7-29:36)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_counts_run_1 (8:9-8:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contigs (22:7-22:28)" +document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_counts_run_2 (14:9-14:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: frac_above_maf_5_percent_well_imputed_threshold (28:7-28:66)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W001::Style/Low] trailing space (18:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genetic_maps_eagle (24:7-24:30)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W001::Style/Low] trailing space (26:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (41:7-41:39)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W001::Style/Low] trailing space (35:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: m3vcf_suffix (34:7-34:48)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W001::Style/Low] trailing space (3:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: merge_ssvcf_mem_mb (27:7-27:36)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W001::Style/Low] trailing space (47:14)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: multi_sample_vcf (14:7-14:29)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W001::Style/Low] trailing space (60:14)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: multi_sample_vcf_index (15:7-15:35)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W001::Style/Low] trailing space (98:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: optional_qc_hwe (20:7-20:29)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: concatenated_output_name (68:9-68:61)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: optional_qc_max_missing (19:7-19:37)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (49:9-49:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_callset_name (25:7-25:33)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (67:9-67:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: perform_extra_qc_steps (18:7-18:45)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (85:9-85:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (21:7-21:20)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: files (69:9-69:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_panel_path (23:7-23:34)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: files (86:9-86:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (38:7-38:26)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (50:9-50:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: single_sample_vcf_indices (17:7-17:45)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_name (51:9-51:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: single_sample_vcfs (16:7-16:38)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: action (10:9-10:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: split_output_to_single_sample (26:7-26:52)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: concatenated_output_name (12:9-12:61)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (37:7-37:24)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (13:9-13:54)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (39:7-39:27)" +document = "chanzuckerberg/czid-workflows:workflows/bulk-download/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: files (11:9-11:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (40:7-40:30)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (403:1-403:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vcf_index_suffix (31:7-31:46)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (502:1-502:1)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestImputation.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vcf_suffix (30:7-30:36)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (964:1-964:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (115:1-115:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (965:1-965:8)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (118:1-118:4)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (113:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (148:1-148:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (132:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (68:1-68:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (154:109)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W001::Style/Low] trailing space (152:15)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (275:89)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W001::Style/Low] trailing space (198:44)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (306:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W001::Style/Low] trailing space (200:57)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (310:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W001::Style/Low] trailing space (202:54)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (312:47)" [[concerns]] kind = "LintWarning" 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"[v1::W001::Style/Low] trailing space (329:67)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: callset_name (13:7-13:26)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (333:11)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cross_check_fingerprints (54:7-54:46)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (334:53)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_resource_vcf (40:7-40:42)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (338:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_resource_vcf_index (41:7-41:54)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (340:15)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf (18:7-18:21)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (343:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf_index (19:7-19:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (465:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: eval_interval_list (29:7-29:30)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (692:109)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: excess_het_threshold (42:7-42:41)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (693:115)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gather_vcfs (47:7-47:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (803:107)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gnarly_scatter_count (51:7-51:36)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W001::Style/Low] trailing space (805:72)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (62:7-62:39)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession_id (363:9-363:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database (28:7-28:30)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: alignments (680:9-680:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hapmap_resource_vcf (30:7-30:31)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly (869:9-869:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hapmap_resource_vcf_index (31:7-31:37)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly (933:9-933:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: huge_disk (23:7-23:20)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (724:9-724:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: indel_filter_level (44:7-44:31)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (870:9-870:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: indel_recalibration_annotation_values (27:7-27:58)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bcftoolsCallTheta (764:9-764:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: indel_recalibration_tranche_values (26:7-26:55)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: call_variants_bam (761:9-761:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: large_disk (22:7-22:21)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cleaned_bam (932:9-932:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: medium_disk (21:7-21:22)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: consensus (797:9-797:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: mills_resource_vcf (36:7-36:30)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1086:9-1086:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: mills_resource_vcf_index (37:7-37:36)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1128:9-1128:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: omni_resource_vcf (32:7-32:29)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (302:9-302:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: omni_resource_vcf_index (33:7-33:35)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (368:9-368:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: one_thousand_genomes_resource_vcf (34:7-34:45)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (444:9-444:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: one_thousand_genomes_resource_vcf_index (35:7-35:51)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (468:9-468:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (17:7-17:20)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (516:9-516:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (15:7-15:21)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (545:9-545:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (16:7-16:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (617:9-617:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rename_gvcf_samples (49:7-49:41)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (655:9-655:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (59:7-59:26)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (683:9-683:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_name_map (14:7-14:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (730:9-730:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: scatter_cross_check_fingerprints (55:7-55:55)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (767:9-767:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: small_disk (20:7-20:21)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (798:9-798:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: snp_filter_level (43:7-43:29)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (829:9-829:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: snp_recalibration_annotation_values (25:7-25:56)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (879:9-879:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: snp_recalibration_tranche_values (24:7-24:53)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (942:9-942:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: snp_vqsr_downsampleFactor (45:7-45:36)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ercc_fasta (514:9-514:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: snps_variant_recalibration_threshold (48:7-48:56)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ercc_stats (934:9-934:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: top_level_scatter_count (46:7-46:35)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (298:9-298:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (58:7-58:24)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (441:9-441:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unbounded_scatter_count_scale_factor (50:7-50:56)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (465:9-465:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unpadded_intervals_file (12:7-12:35)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (513:9-513:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (60:7-60:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (540:9-540:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_allele_specific_annotations (53:7-53:53)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (615:9-615:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_gnarly_genotyper (52:7-52:43)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (652:9-652:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (61:7-61:30)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (824:9-824:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (31:1-31:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (871:9-871:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (41:1-41:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (937:9-937:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (44:1-44:4)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ivarFreqThreshold (726:9-726:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (51:1-51:36)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ivarQualThreshold (728:9-728:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (54:1-54:4)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ivarQualThreshold (763:9-763:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (64:1-64:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kraken2_db_tar_gz (543:9-543:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W001::Style/Low] trailing space (68:15)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_length (443:9-443:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W001::Style/Low] trailing space (88:41)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_reads (300:9-300:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: callset_name (17:7-17:26)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: medaka_model (828:9-828:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (25:7-25:39)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minDepth (727:9-727:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: preemptible_tries (18:7-18:28)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minDepth (765:9-765:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (16:7-16:20)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_length (442:9-442:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (14:7-14:21)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: no_reads_quast (875:9-875:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (15:7-15:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: normalise (827:9-827:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (22:7-22:26)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_loc_db (367:9-367:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_indices_fofn (13:7-13:31)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_s3_path (366:9-366:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: samples_fofn (12:7-12:24)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (365:9-365:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (21:7-21:24)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_s3_path (364:9-364:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (23:7-23:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputFiles (1085:9-1085:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleArrays.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (24:7-24:30)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputFiles (1127:9-1127:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (47:1-47:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (1084:9-1084:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (73:1-73:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (1126:9-1126:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (76:1-76:4)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (297:9-297:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (85:1-85:36)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (440:9-440:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (88:1-88:4)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (464:9-464:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (98:1-98:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (512:9-512:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W001::Style/Low] trailing space (102:15)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (537:9-537:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W001::Style/Low] trailing space (127:44)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (650:9-650:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W001::Style/Low] trailing space (129:43)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (679:9-679:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: batch_id (25:7-25:22)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (722:9-722:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: batch_name (26:7-26:25)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (760:9-760:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq1_input_files (23:7-23:39)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (794:9-794:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq2_input_files (24:7-24:44)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (822:9-822:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gene_ref_flat (14:7-14:25)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (868:9-868:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genome_ref_fasta (12:7-12:28)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (930:9-930:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (41:7-41:39)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: primer_bed (681:9-681:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_index (17:7-17:28)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: primer_schemes (825:9-825:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_name (15:7-15:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: primer_schemes (873:9-873:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_trans_index (18:7-18:34)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: primer_set (826:9-826:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_trans_name (16:7-16:33)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: primer_set (874:9-874:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id_metadata_field (33:7-33:38)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (542:9-542:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_ids (21:7-21:30)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (653:9-653:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_name_metadata_field (32:7-32:40)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (762:9-762:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_names (22:7-22:33)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (796:9-796:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: library (29:7-29:29)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (872:9-872:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: organ (31:7-31:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_host (466:9-466:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: paired_end (34:7-34:25)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_host (938:9-938:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: project_id (27:7-27:32)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samQualThreshold (685:9-685:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: project_name (28:7-28:34)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample (651:9-651:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (38:7-38:26)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample (723:9-723:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rrna_intervals (13:7-13:26)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample (795:9-795:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rsem_ref_index (19:7-19:26)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample (823:9-823:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: species (30:7-30:29)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample (931:9-931:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: stranded (20:7-20:22)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid (539:9-539:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (37:7-37:24)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: technology (299:9-299:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (39:7-39:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: technology (467:9-467:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (40:7-40:30)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: technology (876:9-876:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (41:1-41:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: technology (940:9-940:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (61:1-61:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: threads (877:9-877:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (64:1-64:4)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (935:9-935:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (73:1-73:36)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: apply_length_filter (44:9-44:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (76:1-76:4)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bcftoolsCallTheta (73:9-73:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (86:1-86:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (18:9-18:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W001::Style/Low] trailing space (115:44)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ercc_fasta (19:9-19:94)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W001::Style/Low] trailing space (117:43)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (13:9-13:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W001::Style/Low] trailing space (90:15)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (14:9-14:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: adapter_list (15:7-15:24)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: filter_reads (59:9-59:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: annotations_gtf (14:7-14:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ivarFreqThreshold (62:9-62:39)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: batch_id (20:7-20:22)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ivarQualThreshold (63:9-63:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: batch_name (21:7-21:25)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: kraken2_db_tar_gz (20:9-20:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq1_input_files (18:7-18:39)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_length (49:9-49:79)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq2_input_files (19:7-19:39)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_reads (16:9-16:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genome_ref_fasta (12:7-12:28)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: medaka_model (53:9-53:51)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (35:7-35:39)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minDepth (64:9-64:133)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id_metadata_field (28:7-28:38)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_length (47:9-47:78)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_ids (16:7-16:30)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: no_reads_quast (69:9-69:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_name_metadata_field (27:7-27:40)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: normalise (51:9-51:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_names (17:7-17:33)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_loc_db (78:9-78:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: library (24:7-24:29)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_s3_path (77:9-77:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: organ (26:7-26:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (76:9-76:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: project_id (22:7-22:32)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_s3_path (75:9-75:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: project_name (23:7-23:34)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_bed (28:9-28:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (32:7-32:26)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_refseq (27:9-27:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: species (25:7-25:29)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: prefix (37:9-37:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tar_star_reference (13:7-13:30)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: primer_bed (21:9-21:94)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (31:7-31:24)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: primer_schemes (40:9-40:108)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (33:7-33:27)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: primer_set (41:9-41:43)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (34:7-34:30)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_accession_id (24:9-24:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (108:1-108:36)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (23:9-23:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (111:1-111:4)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_host (30:9-30:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (118:1-118:36)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (81:9-81:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (129:1-129:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample (34:9-34:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (60:1-60:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: technology (31:9-31:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (88:1-88:2)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: trim_adapters (60:9-60:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (91:1-91:4)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" 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-document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_r1_fastq (33:7-33:32)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W004::Style/Medium] mixed indentation characters (770:16-779:5)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_r2_fastq (34:7-34:32)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W004::Style/Medium] mixed indentation characters (801:16-808:5)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_r3_fastq (35:7-35:32)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W004::Style/Medium] mixed indentation characters (882:16-914:5)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: atac_whitelist (45:7-45:95)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1124:6-1124:16)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chrom_sizes (40:7-40:23)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1127:21-1127:32)" [[concerns]] kind = "LintWarning" -document = 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"chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (361:6-361:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: force_no_check (25:7-25:37)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (364:16-364:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestMultiome.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gex_i1_fastq (18:7-18:32)" +document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (366:16-366:26)" [[concerns]] kind = "LintWarning" -document = 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kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestRNAWithUMIsPipeline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: population_vcf (34:7-34:26)" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W001::Style/Low] trailing space (88:10)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestRNAWithUMIsPipeline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: population_vcf_index (35:7-35:32)" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (107:19-107:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestRNAWithUMIsPipeline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r1_fastq 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[[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestRNAWithUMIsPipeline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read2Structure (15:7-15:28)" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (150:6-150:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestRNAWithUMIsPipeline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read_group_name (21:7-21:29)" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (164:19-164:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestRNAWithUMIsPipeline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta 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(196:19-196:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestRNAWithUMIsPipeline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refIndex (28:7-28:20)" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (216:14-216:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestRNAWithUMIsPipeline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (49:7-49:26)" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (224:6-224:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestRNAWithUMIsPipeline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter 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identifier must be snake case (459:19-459:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestReblockGVCF.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (43:1-43:2)" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (95:14-95:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestReblockGVCF.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (46:1-46:4)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (124:1-124:2)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestReblockGVCF.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (53:1-53:36)" +document = 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docker_image_id (216:5-216:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (50:1-50:4)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (247:5-247:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (61:1-61:36)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (280:5-280:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (64:1-64:4)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (311:5-311:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (72:1-72:36)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (347:5-347:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (83:1-83:2)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (381:5-381:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W001::Style/Low] trailing space (132:41)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (38:5-38:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W001::Style/Low] trailing space (134:58)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (418:5-418:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W001::Style/Low] trailing space (136:58)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (454:5-454:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W001::Style/Low] trailing space (87:15)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: annotations_gtf (18:7-18:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (284:5-284:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (316:5-316:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bead_locations (21:7-21:26)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (352:5-352:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: count_exons (20:7-20:26)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (388:5-388:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (28:7-28:39)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (423:5-423:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: i1_fastq (14:7-14:28)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (459:5-459:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id (15:7-15:22)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (283:5-283:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_bam_basename (19:7-19:33)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (315:5-315:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r1_fastq (12:7-12:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (351:5-351:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: r2_fastq (13:7-13:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (387:5-387:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: read_structure (16:7-16:28)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (422:5-422:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (25:7-25:26)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (458:5-458:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tar_star_reference (17:7-17:30)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (7:5-7:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (24:7-24:24)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_ext (9:5-9:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (26:7-26:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genome_dir (45:5-45:46)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSlideSeq.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (27:7-27:30)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_genome (460:5-460:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (102:1-102:2)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_genome (44:5-44:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (41:1-41:2)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: human_bowtie2_genome (424:5-424:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (61:1-61:2)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: human_star_genome (389:5-389:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (64:1-64:4)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lzw_fa (313:5-313:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (77:1-77:36)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_input_fragments (8:5-8:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (80:1-80:4)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_subsample_fragments (353:5-353:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (91:1-91:36)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nucleotide_type (43:5-43:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] trailing space (106:15)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: priceseq_fa (249:5-249:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] trailing space (143:41)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (184:5-184:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] trailing space (145:68)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (217:5-217:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] trailing space (147:43)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (248:5-248:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W001::Style/Low] trailing space (149:50)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (281:5-281:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq1 (26:7-26:18)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (312:5-312:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq2 (27:7-27:19)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (348:5-348:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gene_ref_flat (14:7-14:25)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (382:5-382:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genome_ref_fasta (12:7-12:28)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (39:5-39:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (35:7-35:39)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (419:5-419:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_index (15:7-15:28)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (455:5-455:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_name (18:7-18:29)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_trans_index (16:7-16:34)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: star_genome (42:5-42:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_ref_trans_name (19:7-19:35)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: subsampled_fa (383:5-383:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id (21:7-21:22)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: subsampled_fa (456:5-456:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id_metadata_field (23:7-23:38)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: trimmomatic_fastq (218:5-218:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_name (22:7-22:25)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unmapped_fastq (185:5-185:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_name_metadata_field (24:7-24:40)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unmapped_human_fa (420:5-420:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_name (25:7-25:25)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valid_input_fastq (385:5-385:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: paired_end (28:7-28:25)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valid_input_fastq (41:5-41:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (32:7-32:26)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: validate_input_summary_json (384:5-384:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rrna_intervals (13:7-13:26)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: validate_input_summary_json (40:5-40:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rsem_ref_index (17:7-17:26)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: adapter_fasta (498:5-498:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: stranded (20:7-20:22)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bowtie2_genome (500:5-500:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (31:7-31:24)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (491:5-491:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (33:7-33:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (493:5-493:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestSmartSeq2SingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (34:7-34:30)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (494:5-494:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (106:1-106:36)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (495:5-495:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (109:1-109:4)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_genome (501:5-501:164)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (116:1-116:36)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_genome (497:5-497:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (127:1-127:2)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: human_bowtie2_genome (503:5-503:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (57:1-57:2)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: human_star_genome (502:5-502:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (93:1-93:2)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_input_fragments (504:5-504:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (96:1-96:4)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_subsample_fragments (505:5-505:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] trailing space (131:15)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nucleotide_type (496:5-496:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] trailing space (174:44)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (492:5-492:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] trailing space (176:57)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: star_genome (499:5-499:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] trailing space (178:54)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (166:10-166:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] trailing space (180:50)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (168:11-168:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W001::Style/Low] trailing space (182:57)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (181:6-181:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: annotation_intervals (34:7-34:39)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (184:12-184:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: call_sample_name (31:7-31:30)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (204:10-204:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: callset_name (13:7-13:26)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (205:11-205:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cross_check_fingerprints (43:7-43:46)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (214:6-214:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf (18:7-18:21)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (217:12-217:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf_index (19:7-19:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (235:10-235:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: eval_interval_list (25:7-25:30)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (236:11-236:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: excess_het_threshold (26:7-26:41)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (245:6-245:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: flow_order (35:7-35:24)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (248:12-248:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gather_vcfs (41:7-41:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (266:10-266:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (51:7-51:39)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (267:11-267:20)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_database (24:7-24:30)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:10-26:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: huge_disk (23:7-23:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (278:6-278:12)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: indel_annotations (37:7-37:31)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:11-27:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: large_disk (22:7-22:28)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (281:12-281:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: medium_disk (21:7-21:28)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (300:10-300:17)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: model_backend (39:7-39:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (301:11-301:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (17:7-17:20)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (309:6-309:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (15:7-15:21)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (312:12-312:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (16:7-16:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (317:10-317:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_sdf (32:7-32:25)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (334:10-334:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (48:7-48:26)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (335:11-335:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: runs_file (33:7-33:21)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (336:11-336:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_name_map (14:7-14:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (345:6-345:18)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: scatter_cross_check_fingerprints (44:7-44:55)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (348:12-348:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: small_disk (20:7-20:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (349:17-349:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: snp_annotations (36:7-36:29)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:6-36:13)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: top_level_scatter_count (40:7-40:35)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (379:6-379:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_highconf_intervals (30:7-30:36)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (382:12-382:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (47:7-47:24)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (39:12-39:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_sample_name (27:7-27:31)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf (28:7-28:21)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (416:6-416:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_vcf_index (29:7-29:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (419:12-419:21)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unbounded_scatter_count_scale_factor (42:7-42:56)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (424:10-424:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unpadded_intervals_file (12:7-12:35)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (441:10-441:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (49:7-49:27)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (442:11-442:29)" [[concerns]] kind = "LintWarning" -document = 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"LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (63:1-63:36)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (503:12-503:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (66:1-66:4)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (625:10-625:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (79:1-79:36)" +document = 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"[v1::W006::Naming/Low] identifier must be snake case (638:10-638:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: alignment_references (13:7-13:47)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (639:11-639:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (17:7-17:28)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (644:10-644:25)" [[concerns]] kind = "LintWarning" -document = 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missing parameter meta within workflow: input_bam_list (16:7-16:34)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (648:11-648:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram_list (15:7-15:35)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (649:11-649:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reads_per_split (19:7-19:37)" +document = 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(660:11-660:47)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: save_bam_file (20:7-20:36)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (661:11-661:47)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (23:7-23:24)" +document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (662:11-662:52)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl" 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"LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (51:1-51:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (726:9-726:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (54:1-54:4)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (740:9-740:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (75:1-75:36)" 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[[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W001::Style/Low] trailing space (106:15)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotated_merged_fa (889:9-889:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W001::Style/Low] trailing space (155:50)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotated_merged_fa (903:9-903:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W001::Style/Low] trailing space (157:43)" +document = 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= "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_taxid_annot_fasta (938:9-938:48)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (18:7-18:28)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (1221:9-1221:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination_sites (12:7-12:45)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (1235:9-1235:44)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: filtering_model_no_gt_name (23:7-23:78)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (1222:9-1222:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (30:7-30:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (1236:9-1236:41)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam_list (17:7-17:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (1223:9-1223:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram_list (16:7-16:35)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (1237:9-1237:37)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: make_haplotype_bam (21:7-21:41)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fasta (1056:9-1056:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: merge_bam_file (20:7-20:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fasta (1070:9-1070:27)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reads_per_split (22:7-22:37)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (1142:9-1142:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (27:7-27:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (1156:9-1156:38)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rsq_threshold (19:7-19:32)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (551:9-551:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (26:7-26:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (597:9-597:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (28:7-28:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1015:9-1015:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: variant_calling_settings (14:7-14:54)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1029:9-1029:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (29:7-29:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1095:9-1095:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vcf_post_processing (15:7-15:44)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1109:9-1109:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (102:1-102:4)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (720:9-720:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (116:1-116:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (734:9-734:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (127:1-127:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (767:9-767:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (51:1-51:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (781:9-781:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (81:1-81:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (970:9-970:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (84:1-84:4)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (984:9-984:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (99:1-99:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (598:9-598:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] trailing space (131:15)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1020:9-1020:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] trailing space (175:41)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1034:9-1034:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] trailing space (177:41)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1058:9-1058:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] trailing space (179:81)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1072:9-1072:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] trailing space (181:92)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1102:9-1102:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W001::Style/Low] trailing space (183:50)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1116:9-1116:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: analysis_version_number (13:7-13:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1143:9-1143:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bead_pool_manifest_file (24:7-24:35)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (114:9-114:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: call_rate_threshold (14:7-14:32)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1157:9-1157:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chain_file (30:7-30:22)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1181:9-1181:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chip_manifest_csv_file (26:7-26:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1195:9-1195:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chip_type (25:7-25:67)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1225:9-1225:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chip_well_barcode (16:7-16:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1239:9-1239:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cluster_file (31:7-31:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (171:9-171:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: control_sample_intervals_file (34:7-34:41)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (203:9-203:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: control_sample_name (35:7-35:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (266:9-266:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: control_sample_vcf_file (32:7-32:35)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (302:9-302:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: control_sample_vcf_index_file (33:7-33:41)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (333:9-333:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbSNP_vcf (22:7-22:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (391:9-391:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbSNP_vcf_index (23:7-23:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (428:9-428:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: disk_size (37:7-37:20)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (485:9-485:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (45:7-45:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (516:9-516:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: green_idat_cloud_path (18:7-18:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (53:9-53:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: indel_genotype_concordance_threshold (36:7-36:49)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (558:9-558:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: preemptible_tries (38:7-38:28)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (603:9-603:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: red_idat_cloud_path (17:7-17:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (647:9-647:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (21:7-21:20)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (649:9-649:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (19:7-19:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (683:9-683:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (20:7-20:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (692:9-692:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reported_gender (15:7-15:29)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (728:9-728:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (42:7-42:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (742:9-742:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_alias (12:7-12:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (775:9-775:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: supported_ref_dict (29:7-29:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (789:9-789:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: supported_ref_fasta (27:7-27:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (815:9-815:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: supported_ref_fasta_index (28:7-28:37)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (829:9-829:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (41:7-41:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (859:9-859:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (43:7-43:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (873:9-873:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestValidateChip.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (44:7-44:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (893:9-893:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (107:1-107:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (8:9-8:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (47:1-47:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (907:9-907:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (73:1-73:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (925:9-925:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (76:1-76:4)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (939:9-939:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (86:1-86:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (975:9-975:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (89:1-89:4)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (989:9-989:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (96:1-96:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: guppy_basecaller_setting (331:9-331:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W001::Style/Low] trailing space (111:15)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (111:9-111:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W001::Style/Low] trailing space (136:43)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (170:9-170:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W001::Style/Low] trailing space (138:54)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (200:9-200:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: agg_preemptible_tries (29:7-29:32)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (264:9-264:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (27:7-27:28)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (301:9-301:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: break_bands_at_multiples_of (17:7-17:38)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (330:9-330:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: calling_interval_list (14:7-14:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (426:9-426:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contamination (18:7-18:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (52:9-52:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf (25:7-25:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (7:9-7:25)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dbsnp_vcf_index (26:7-26:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (811:9-811:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: evaluation_interval_list (15:7-15:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (825:9-825:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: final_vcf_base_name (28:7-28:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (1180:9-1180:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (41:7-41:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (1194:9-1194:31)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: haplotype_scatter_count (16:7-16:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: library_type (112:9-112:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (19:7-19:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: library_type (201:9-201:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam_index (20:7-20:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1014:9-1014:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: make_bamout (31:7-31:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1028:9-1028:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: make_gvcf (30:7-30:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1094:9-1094:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_dict (23:7-23:20)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1108:9-1108:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (21:7-21:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (647:9-647:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta_index (22:7-22:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (690:9-690:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_str (24:7-24:20)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (725:9-725:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (38:7-38:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (739:9-739:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: run_dragen_mode_variant_calling (12:7-12:54)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (772:9-772:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: skip_reblocking (33:7-33:38)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (786:9-786:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (37:7-37:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (892:9-892:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (39:7-39:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (906:9-906:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_dragen_hard_filtering (34:7-34:48)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (969:9-969:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_gatk3_haplotype_caller (32:7-32:49)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (983:9-983:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_spanning_event_genotyping (13:7-13:51)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (600:9-600:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestVariantCalling.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (40:7-40:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_minimap2_index (554:9-554:35)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: allow_empty_ref_alt (33:5-33:40)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (727:9-727:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dragen_functional_equivalence_mode (25:5-25:55)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (741:9-741:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dragen_maximum_quality_mode (26:5-26:48)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (774:9-774:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: dragmap_reference (13:5-13:40)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (788:9-788:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_file (17:5-17:37)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_args (552:9-552:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_index (18:5-18:38)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap_host_db (113:9-113:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (41:5-41:37)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap_human_db (202:9-202:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: papi_settings (15:5-15:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: non_contig_reads_fa (514:9-514:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: perform_bqsr (31:5-31:32)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (1092:9-1092:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: provide_bam_output (22:5-22:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (1106:9-1106:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: references (12:5-12:44)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1013:9-1013:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (38:5-38:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1027:9-1027:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: run_dragen_mode_variant_calling (28:5-28:52)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1091:9-1091:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_and_unmapped_bams (11:5-11:51)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1105:9-1105:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: scatter_settings (14:5-14:51)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (813:9-813:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (37:5-37:22)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (827:9-827:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unmap_contaminant_reads (30:5-30:43)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (891:9-891:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (39:5-39:25)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (905:9-905:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_bwa_mem (32:5-32:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (682:9-682:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_dragen_hard_filtering (34:5-34:46)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (689:9-689:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_gatk3_haplotype_caller (23:5-23:46)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1012:9-1012:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_spanning_event_genotyping (29:5-29:49)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1026:9-1026:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (40:5-40:28)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1090:9-1090:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: wgs_coverage_interval_list (20:5-20:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1104:9-1104:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (121:1-121:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (858:9-858:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (132:1-132:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (872:9-872:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (39:1-39:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_top_m8 (765:9-765:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (57:1-57:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_top_m8 (779:9-779:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (60:1-60:4)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (1088:9-1088:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (86:1-86:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (1102:9-1102:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (89:1-89:4)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1087:9-1087:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] trailing space (136:15)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1101:9-1101:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] trailing space (185:50)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1219:9-1219:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] trailing space (187:43)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1233:9-1233:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] trailing space (189:43)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (812:9-812:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] trailing space (191:43)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (826:9-826:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] trailing space (193:54)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (890:9-890:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W001::Style/Low] trailing space (195:44)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (904:9-904:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: base_file_name (16:7-16:28)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (968:9-968:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta (19:7-19:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (982:9-982:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cram_ref_fasta_index (20:7-20:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (1224:9-1224:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: final_gvcf_base_name (17:7-17:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (1238:9-1238:24)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_file (24:7-24:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8 (646:9-646:19)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fingerprint_genotypes_index (25:7-25:40)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1086:9-1086:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (33:7-33:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1100:9-1100:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_bam (13:7-13:22)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1218:9-1218:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_cram (12:7-12:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1232:9-1232:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_map (14:7-14:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (857:9-857:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: papi_settings (23:7-23:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (871:9-871:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: references (21:7-21:46)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (967:9-967:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (30:7-30:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (981:9-981:30)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_name (15:7-15:25)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (1220:9-1220:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: scatter_settings (22:7-22:53)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (1234:9-1234:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (29:7-29:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (718:9-718:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: unmapped_bam_suffix (18:7-18:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (732:9-732:23)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (31:7-31:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: polishing_iterations (332:9-332:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (32:7-32:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pre_alignment_fasta (856:9-856:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestWholeGenomeReprocessing.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: wgs_coverage_interval_list (26:7-26:38)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pre_alignment_fasta (870:9-870:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (31:1-31:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (555:9-555:22)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (41:1-41:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_contig_sam (1057:9-1057:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (44:1-44:4)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_contig_sam (1071:9-1071:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (57:1-57:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (1011:9-1011:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (69:1-69:4)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (1025:9-1025:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (79:1-79:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (719:9-719:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W001::Style/Low] trailing space (108:41)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (733:9-733:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W001::Style/Low] trailing space (110:59)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (766:9-766:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W001::Style/Low] trailing space (83:15)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (780:9-780:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bin_size_list (18:7-18:37)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (966:9-966:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genome_name (15:7-15:25)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (980:9-980:32)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (25:7-25:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contig_tsv (390:9-390:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_fastq1 (12:7-12:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contig_tsv (484:9-484:33)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_fastq2 (13:7-13:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contigs_sam (389:9-389:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_id (14:7-14:22)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contigs_tsv (814:9-814:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_reference (16:7-16:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contigs_tsv (828:9-828:34)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_bam (17:7-17:52)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (553:9-553:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (22:7-22:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (599:9-599:36)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (21:7-21:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (557:9-557:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (23:7-23:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (602:9-602:26)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestscATAC.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (24:7-24:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: subsample_depth (265:9-265:28)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (34:1-34:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1017:9-1017:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (47:1-47:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1031:9-1031:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (50:1-50:4)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1097:9-1097:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (61:1-61:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1111:9-1111:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (64:1-64:4)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (722:9-722:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (74:1-74:2)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (736:9-736:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W001::Style/Low] trailing space (78:15)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (769:9-769:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W001::Style/Low] trailing space (97:64)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (783:9-783:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: chromosome_sizes (20:7-20:28)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (972:9-972:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_input_read1 (12:7-12:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (986:9-986:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastq_input_read2 (13:7-13:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1016:9-1016:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: genome_fa (21:7-21:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1030:9-1030:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: google_account_vault_path (28:7-28:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1096:9-1096:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: mapping_yaml (18:7-18:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1110:9-1110:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_basename (16:7-16:40)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (721:9-721:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: plate_id (15:7-15:22)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (735:9-735:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: random_primer_indexes (14:7-14:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (768:9-768:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: results_path (25:7-25:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (782:9-782:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: snakefile (19:7-19:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (971:9-971:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: tarred_index_files (17:7-17:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (985:9-985:29)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: truth_path (24:7-24:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1018:9-1018:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: update_truth (26:7-26:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1032:9-1032:40)" [[concerns]] kind = "LintWarning" -document = "broadinstitute/warp:verification/test-wdls/TestsnM3C.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: vault_token_path (27:7-27:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1099:9-1099:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (274:1-274:12)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1113:9-1113:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (280:1-280:8)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (723:9-723:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (317:1-317:8)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: 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"[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1114:9-1114:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (427:1-427:12)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (724:9-724:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (429:1-429:12)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (738:9-738:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] line contains 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (1288:9-1288:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (533:1-533:8)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (1278:9-1278:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (103:25)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (1292:9-1292:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (113:26)" 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= "[v1::W001::Style/Low] trailing space (135:20)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (1299:9-1299:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (136:15)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (1271:9-1271:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (250:16)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (1285:9-1285:36)" [[concerns]] kind = "LintWarning" 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guppy_basecaller_setting (1261:9-1261:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (495:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: guppy_basecaller_setting (1275:9-1275:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (499:16)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_fastq (1258:9-1258:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (509:91)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_fastq (1272:9-1272:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (511:13)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: library_type (1260:9-1260:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (521:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: library_type (1274:9-1274:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (527:27)" +document = 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"[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (1297:9-1297:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (750:6)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_host_db (1265:9-1265:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (88:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_host_db (1279:9-1279:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W001::Style/Low] trailing space (94:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_human_db (1266:9-1266:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: amr_kmer_db (494:9-494:25)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_human_db (1280:9-1280:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: amr_kmer_db (526:9-526:25)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (1279:9-1279:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: card_json (492:9-492:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (1293:9-1293:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: card_json (524:9-524:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: polishing_iterations (1268:9-1268:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: card_json (557:9-557:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: polishing_iterations (1282:9-1282:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: card_json (583:9-583:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (1256:9-1256:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: card_ontology (246:9-246:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (1270:9-1270:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_sizes (183:9-183:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: subsample_depth (1263:9-1263:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: clusters (182:9-182:22)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: subsample_depth (1277:9-1277:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fa (556:9-556:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (1275:9-1275:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fa (647:9-647:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (1289:9-1289:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fa (755:9-755:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_whitelist (1276:9-1276:113)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (184:9-184:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_whitelist (1290:9-1290:113)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (247:9-247:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (1288:9-1288:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (497:9-497:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (1302:9-1302:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (529:9-529:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (1289:9-1289:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (558:9-558:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (1303:9-1303:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (584:9-584:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1023:6-1023:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (612:9-612:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1026:14-1026:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (652:9-652:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1068:6-1068:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (697:9-697:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1098:6-1098:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (757:9-757:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (109:6-109:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: final_summary (756:9-756:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1100:14-1100:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gene_coverage (245:9-245:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1104:14-1104:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filtered_reads (180:9-180:41)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1143:14-1143:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: intermediate_files (651:9-651:40)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1144:14-1144:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kma_output (243:9-243:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1154:6-1154:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kma_species_output (244:9-244:32)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1192:6-1192:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kmer_db (493:9-493:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1230:6-1230:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kmer_db (525:9-525:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1232:14-1232:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_amr_results (695:9-695:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1234:14-1234:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_output (241:9-241:25)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1270:17-1270:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_output_json (491:9-491:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1284:15-1284:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_output_json (696:9-696:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1288:14-1288:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_reports (649:9-649:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1295:17-1295:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: main_species_output (242:9-242:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1296:16-1296:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_contig_length (611:9-611:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1297:16-1297:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: non_host_reads_fa (582:9-582:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1616:14-1616:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: non_host_reads_fa (648:9-648:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1618:14-1618:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: output_sorted_length_100 (523:9-523:38)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (168:6-168:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: raw_reports (650:9-650:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (198:6-198:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reduplicated_reads (610:9-610:40)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (262:6-262:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_name (248:9-248:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (299:6-299:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: subsampled_reads (181:9-181:38)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (328:6-328:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wildcard_data (495:9-495:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (387:6-387:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wildcard_data (527:9-527:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (424:6-424:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wildcard_index (496:9-496:28)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (481:6-481:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: wildcard_index (528:9-528:28)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:6-50:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: amr_kmer_db (28:9-28:92)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (512:6-512:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: card_json (25:9-25:81)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (548:6-548:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: card_ontology (26:9-26:97)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (552:16-552:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (22:9-22:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (554:15-554:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: filtered_sample (21:9-21:40)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (557:17-557:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filtering_docker_image_id (24:9-24:71)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (586:14-586:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: kmer_db (27:9-27:85)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (594:6-594:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_contig_length (31:9-31:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (5:6-5:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: raw_sample (20:9-20:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (602:17-602:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (33:9-33:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (635:14-635:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample_name (23:9-23:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (644:6-644:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: wildcard_data (29:9-29:106)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (646:14-646:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/amr/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: wildcard_index (30:9-30:106)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (648:14-648:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (103:1-103:8)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (678:14-678:23)" 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parameter meta within task: query_1 (29:9-29:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (222:13)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: db_chunk (8:9-8:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (227:14)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (9:9-9:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (228:32)" +document = 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"[v1::W003::Completeness/Medium] missing parameter meta within task: cut_height (245:9-245:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (6:12)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: distances (327:9-327:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (72:32)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (120:9-120:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_fasta (143:9-143:26)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (190:9-190:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_summary (142:9-142:28)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (210:9-210:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbtype (145:9-145:22)" +document = 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docker_image_id (329:9-329:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ground_truth_nr (187:9-187:30)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (352:9-352:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ground_truth_nt (186:9-186:30)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (375:9-375:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_nr (183:9-183:34)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (397:9-397:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_nt (182:9-182:34)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: newick (373:9-373:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_ref_nr (185:9-185:39)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_loc_db (119:9-119:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_ref_nt (184:9-184:39)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_s3_path (118:9-118:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: step_counts (188:9-188:26)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (117:9-117:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxadb_sqlite (144:9-144:28)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_s3_path (116:9-116:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_counts (141:9-141:26)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_accession_ids (396:9-396:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_fasta_run_1 (9:9-9:32)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_taxon_id (188:9-188:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_fasta_run_2 (15:9-15:33)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_and_reference_fastas (208:9-208:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_summary_run_1 (8:9-8:34)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (189:9-189:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_summary_run_2 (14:9-14:35)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (246:9-246:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (24:9-24:31)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (328:9-328:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ground_truth (22:9-22:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (351:9-351:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: step_counts_run_1 (11:9-11:39)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (374:9-374:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: step_counts_run_2 (17:9-17:39)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ska_align_p (276:9-276:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_counts_run_1 (7:9-7:32)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ska_distances (244:9-244:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/long-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_counts_run_2 (13:9-13:33)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ska_hashes (275:9-275:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W001::Style/Low] trailing space (12:20)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: superkingdom_name (209:9-209:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W001::Style/Low] trailing space (48:19)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: variants (350:9-350:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W001::Style/Low] trailing space (66:23)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: additional_reference_accession_ids (19:9-19:62)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W001::Style/Low] trailing space (71:31)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cut_height (26:9-26:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W001::Style/Low] trailing space (82:30)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (28:9-28:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W001::Style/Low] trailing space (96:13)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_loc_db (24:9-24:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbtype (70:9-70:22)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_s3_path (23:9-23:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (35:9-35:31)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (22:9-22:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (50:9-50:31)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_s3_path (21:9-21:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (6:9-6:31)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_taxon_id (14:9-14:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (71:9-71:31)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (31:9-31:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ground_truth (69:9-69:26)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: samples (13:9-13:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa (68:9-68:31)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ska_align_p (27:9-27:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sc (34:9-34:23)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: superkingdom_name (16:9-16:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/mngs-benchmark-tasks.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: step_counts (5:9-5:32)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (113:6-113:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W001::Style/Low] trailing space (13:39)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (116:16-116:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W001::Style/Low] trailing space (23:29)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (118:16-118:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W001::Style/Low] trailing space (27:45)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (177:6-177:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W001::Style/Low] trailing space (28:87)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (206:6-206:12)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W001::Style/Low] trailing space (29:44)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (21:16-21:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W001::Style/Low] trailing space (30:19)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:16-23:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W001::Style/Low] trailing space (40:32)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (242:6-242:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W001::Style/Low] trailing space (43:44)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (272:6-272:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W001::Style/Low] trailing space (44:87)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:16-31:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W001::Style/Low] trailing space (45:43)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (325:6-325:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W001::Style/Low] trailing space (46:19)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (348:6-348:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W001::Style/Low] trailing space (56:32)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (371:6-371:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_fasta_run_1 (11:9-11:33)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (394:6-394:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_fasta_run_2 (17:9-17:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (162:5-162:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_summary_run_1 (10:9-10:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (163:5-163:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_summary_run_2 (16:9-16:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (164:5-164:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (24:9-24:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (121:5-121:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ground_truth (21:9-21:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (157:5-157:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: step_counts_run_1 (13:9-13:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (193:5-193:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: step_counts_run_2 (19:9-19:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (36:5-36:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_counts_run_1 (9:9-9:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_counts_run_2 (15:9-15:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (76:5-76:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: workflow_type (23:9-23:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (197:5-197:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (104:1-104:8)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (123:5-123:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (171:1-171:8)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (195:5-195:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (19:1-19:8)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_ext (124:5-124:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (201:1-201:4)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8_gsnap_deduped_m8 (165:5-165:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (217:1-217:4)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8_gsnap_deduped_m8 (78:5-78:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (31:1-31:4)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (10:5-10:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (81:1-81:8)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nonhost_fasta_refined_taxid_annot_fasta (196:5-196:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (93:1-93:2)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_db (92:5-92:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (102:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (166:5-166:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (112:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (93:5-93:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (116:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_blast_top_m8 (161:5-161:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (117:15)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_hitsummary2_tab (160:5-160:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (12:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_reassigned_m8 (159:5-159:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (142:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: resist_genome_bed (126:5-126:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (146:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: resist_genome_db (125:5-125:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (149:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (122:5-122:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (162:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (158:5-158:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (163:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (194:5-194:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (164:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (37:5-37:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (165:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (174:13)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (77:5-77:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (182:16)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_fasta (38:5-38:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (185:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_family_nr_fasta (89:5-89:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (20:56)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_family_nt_fasta (87:5-87:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (212:102)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_genus_nr_fasta (85:5-85:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (224:13)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_genus_nt_fasta (83:5-83:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (230:14)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_nr_fasta (81:5-81:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (231:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_nt_fasta (79:5-79:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (23:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_fasta_in_annotated_merged_fa (7:5-7:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (28:15)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_fasta_in_gsnap_hitsummary_tab (8:5-8:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (33:15)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_fasta_in_rapsearch2_hitsummary_tab (9:5-9:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (42:15)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_combined_json (91:5-91:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (52:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_family_nr_json (90:5-90:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (55:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_family_nt_json (88:5-88:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (58:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_genus_nr_json (86:5-86:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (65:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_genus_nt_json (84:5-84:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (73:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_nr_json (82:5-82:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W001::Style/Low] trailing space (7:12)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_nt_json (80:5-80:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_fasta (146:9-146:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (198:5-198:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_summary (145:9-145:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_coverage_json (234:5-234:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dbtype (148:9-148:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_stats_json (235:5-235:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (149:9-149:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contigs_fasta (236:5-236:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (191:9-191:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (225:5-225:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ground_truth_nr (189:9-189:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_clusters_csv (240:5-240:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ground_truth_nt (188:9-188:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (237:5-237:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_nr (185:9-185:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (238:5-238:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_nt (184:9-184:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (241:5-241:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_ref_nr (187:9-187:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_m8_gsnap_deduped_m8 (230:5-230:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: preprocessed_taxa_ref_nt (186:9-186:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (245:5-245:90)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: step_counts (190:9-190:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nonhost_fasta_refined_taxid_annot_fasta (239:5-239:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxadb_sqlite (147:9-147:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_db (242:5-242:76)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_counts (144:9-144:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (244:5-244:89)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_fasta_run_1 (10:9-10:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (243:5-243:87)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_fasta_run_2 (16:9-16:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_blast_top_m8 (233:5-233:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_summary_run_1 (9:9-9:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_hitsummary2_tab (232:5-232:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_summary_run_2 (15:9-15:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_reassigned_m8 (231:5-231:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (25:9-25:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_bed (247:5-247:83)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ground_truth (23:9-23:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_db (246:5-246:80)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: step_counts_run_1 (12:9-12:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (226:5-226:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: step_counts_run_2 (18:9-18:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_annotated_merged_fa (227:5-227:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_counts_run_1 (8:9-8:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_gsnap_hitsummary_tab (228:5-228:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/benchmark/short-read-mngs-benchmark.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_counts_run_2 (14:9-14:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_rapsearch2_hitsummary_tab (229:5-229:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (403:1-403:20)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (248:5-248:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (502:1-502:1)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:6-119:14)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (964:1-964:8)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (122:12-122:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (113:13)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (143:10-143:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (132:13)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (144:10-144:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (154:109)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (147:10-147:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (275:89)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (155:6-155:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (306:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (158:12-158:21)" [[concerns]] kind = "LintWarning" -document = 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"LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (324:15)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (165:10-165:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (329:67)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (191:6-191:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (333:11)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (194:12-194:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (334:53)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (214:10-214:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (338:43)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (215:11-215:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (340:15)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (226:12-226:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (343:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (229:10-229:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (465:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (230:10-230:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (692:109)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (231:10-231:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (693:115)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (232:10-232:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (803:107)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (233:10-233:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W001::Style/Low] trailing space (805:72)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (343:10-343:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession_id (363:9-363:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (344:10-344:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: alignments (680:9-680:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (345:10-345:60)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly (869:9-869:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (346:10-346:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly (933:9-933:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (347:10-347:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (724:9-724:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (348:10-348:51)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (870:9-870:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (349:11-349:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bcftoolsCallTheta (764:9-764:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:6-34:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: call_variants_bam (761:9-761:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (352:10-352:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cleaned_bam (932:9-932:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (353:11-353:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: consensus (797:9-797:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:12-37:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1086:9-1086:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (302:9-302:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (6:12-6:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (368:9-368:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (74:6-74:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (444:9-444:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (77:12-77:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (468:9-468:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (78:10-78:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (516:9-516:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (545:9-545:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: adapter_fasta (351:5-351:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (617:9-617:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (868:5-868:13)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (655:9-655:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_ercc_filtered1_fastq (349:5-349:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (683:9-683:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_ercc_filtered2_fastq (350:5-350:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (730:9-730:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_host_filtered1_fastq (626:5-626:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (767:9-767:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_host_filtered2_fastq (627:5-627:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (798:9-798:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_human_filtered1_fastq (795:5-795:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (829:9-829:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_human_filtered2_fastq (796:5-796:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (879:9-879:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_options (259:5-259:54)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (942:9-942:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_options (543:5-543:54)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ercc_fasta (514:9-514:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_options (724:5-724:54)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ercc_stats (934:9-934:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (262:5-262:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (298:9-298:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (359:5-359:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (441:9-441:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (428:5-428:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (465:9-465:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (546:5-546:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (513:9-513:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (634:5-634:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (540:9-540:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (727:5-727:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (615:9-615:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (803:5-803:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (652:9-652:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup1_fastq (947:5-947:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (824:9-824:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup2_fastq (948:5-948:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (871:9-871:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (220:5-220:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (937:9-937:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (261:5-261:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ivarFreqThreshold (726:9-726:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (358:5-358:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ivarQualThreshold (728:9-728:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (427:5-427:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ivarQualThreshold (763:9-763:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (545:5-545:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kraken2_db_tar_gz (543:9-543:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (633:5-633:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_length (443:9-443:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (726:5-726:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_reads (300:9-300:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (802:5-802:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: medaka_model (828:9-828:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (869:5-869:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minDepth (727:9-727:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (913:5-913:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minDepth (765:9-765:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (952:5-952:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_length (442:9-442:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (949:5-949:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: no_reads_quast (875:9-875:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ercc_index_tar (258:5-258:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: normalise (827:9-827:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp1_fastq (419:5-419:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_loc_db (367:9-367:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp1_fastq (538:5-538:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_s3_path (366:9-366:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp2_fastq (420:5-420:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (365:9-365:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp2_fastq (539:5-539:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_s3_path (364:9-364:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp_options (354:5-356:82)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outputFiles (1085:9-1085:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_ext (216:5-216:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (1084:9-1084:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_filtered1_fastq (911:5-911:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (297:9-297:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_filtered2_fastq (912:5-912:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (440:9-440:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_host_filtered1_fastq (719:5-719:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (464:9-464:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_host_filtered2_fastq (720:5-720:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (512:9-512:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_options (631:5-631:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (537:9-537:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_options (800:5-800:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (650:9-650:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (542:5-542:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (679:9-679:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (630:5-630:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (722:9-722:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (723:5-723:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (760:9-760:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (799:5-799:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (794:9-794:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kallisto_idx (421:5-421:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (822:9-822:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kallisto_options (425:5-425:54)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (868:9-868:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_input_fragments (218:5-218:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (930:9-930:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_subsample_fragments (950:5-950:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: primer_bed (681:9-681:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads1_fastq (214:5-214:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: primer_schemes (825:9-825:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads2_fastq (215:5-215:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: primer_schemes (873:9-873:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (221:5-221:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: primer_set (826:9-826:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (914:5-914:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: primer_set (874:9-874:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (953:5-953:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (542:9-542:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valid_input1_fastq (254:5-254:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (653:9-653:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valid_input2_fastq (255:5-255:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (762:9-762:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: adapter_fasta (14:5-14:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (796:9-796:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bowtie2_index_tar (17:5-17:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_fasta (872:9-872:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cpu (32:5-32:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_host (466:9-466:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (33:5-33:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ref_host (938:9-938:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ercc_index_tar (27:5-27:117)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samQualThreshold (685:9-685:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (10:5-10:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample (651:9-651:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (11:5-11:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample (723:9-723:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (36:5-36:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample (795:9-795:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gtf_gz (22:5-22:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample (823:9-823:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_index_tar (18:5-18:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample (931:9-931:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_genome (16:5-16:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid (539:9-539:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: human_bowtie2_index_tar (24:5-24:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: technology (299:9-299:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: human_hisat2_index_tar (25:5-25:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: technology (467:9-467:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: kallisto_idx (19:5-19:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: technology (876:9-876:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_input_fragments (29:5-29:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: technology (940:9-940:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_subsample_fragments (30:5-30:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: threads (877:9-877:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nucleotide_type (12:5-12:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: vcf (935:9-935:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (37:5-37:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: apply_length_filter (44:9-44:43)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (133:8-133:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bcftoolsCallTheta (73:9-73:41)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (134:9-134:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (18:9-18:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (161:10-161:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ercc_fasta (19:9-19:94)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (162:11-162:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (13:9-13:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (166:10-166:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (14:9-14:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (167:11-167:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: filter_reads (59:9-59:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (168:10-168:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ivarFreqThreshold (62:9-62:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (169:10-169:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ivarQualThreshold (63:9-63:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (171:10-171:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: kraken2_db_tar_gz (20:9-20:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (172:11-172:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_length (49:9-49:79)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (178:10-178:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_reads (16:9-16:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (17:10-17:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: medaka_model (53:9-53:51)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (181:10-181:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minDepth (64:9-64:133)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (182:11-182:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_length (47:9-47:78)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (183:10-183:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: no_reads_quast (69:9-69:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (184:10-184:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: normalise (51:9-51:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (185:10-185:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_loc_db (78:9-78:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (186:11-186:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_s3_path (77:9-77:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (187:10-187:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (76:9-76:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (18:10-18:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_s3_path (75:9-75:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (192:11-192:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_bed (28:9-28:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (193:11-193:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: output_refseq (27:9-27:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (194:11-194:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: prefix (37:9-37:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (195:11-195:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: primer_bed (21:9-21:94)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (196:11-196:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: primer_schemes (40:9-40:108)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (197:11-197:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: primer_set (41:9-41:43)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (199:10-199:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_accession_id (24:9-24:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (200:11-200:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_fasta (23:9-23:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (212:6-212:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ref_host (30:9-30:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (214:10-214:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (81:9-81:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (215:11-215:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: sample (34:9-34:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (221:12-221:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: technology (31:9-31:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (239:10-239:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: trim_adapters (60:9-60:37)" +document = 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identifier must be snake case (259:12-259:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W004::Style/Medium] mixed indentation characters (548:16-601:5)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:10-25:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W004::Style/Medium] mixed indentation characters (620:16-635:5)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (267:10-267:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/consensus-genome/run.wdl" -message = "[v1::W004::Style/Medium] mixed indentation characters (688:16-706:5)" +document = 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[[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/diamond/diamond.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (33:9-33:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (404:10-404:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/diamond/diamond.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: extra_args (31:9-31:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (405:11-405:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/diamond/diamond.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: query_0 (29:9-29:21)" +document = 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"chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (724:12-724:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" -message = "[v1::W001::Style/Low] trailing space (418:15)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (732:10-732:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" -message = "[v1::W001::Style/Low] trailing space (88:10)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (780:10-780:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (124:1-124:2)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (781:11-781:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (200:1-200:2)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (792:6-792:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W001::Style/Low] trailing space (111:51)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (795:10-795:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W001::Style/Low] trailing space (114:52)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (796:11-796:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W001::Style/Low] trailing space (139:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (800:12-800:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W001::Style/Low] trailing space (141:5)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (808:10-808:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W001::Style/Low] trailing space (156:41)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (855:10-855:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W001::Style/Low] trailing space (162:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (856:11-856:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W001::Style/Low] trailing space (50:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (909:6-909:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W001::Style/Low] trailing space (72:42)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (911:10-911:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W001::Style/Low] trailing space (79:147)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (912:11-912:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: adapter_fasta (186:5-186:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (914:12-914:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_fa (349:5-349:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (932:10-932:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_genome (317:5-317:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (933:11-933:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup_fa (282:5-282:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (945:6-945:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup_fa (314:5-314:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (947:10-947:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup_fa (350:5-350:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (948:11-948:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup_fa (386:5-386:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (953:12-953:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup_fa (421:5-421:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (19:9-19:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup_fa (457:5-457:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (18:9-18:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (183:5-183:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (14:9-14:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (216:5-216:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (15:9-15:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (247:5-247:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (16:9-16:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (280:5-280:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (17:9-17:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (311:5-311:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: non_host_gsnap_genome_name (20:9-20:53)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (347:5-347:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (21:9-21:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (381:5-381:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (17:14-17:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (38:5-38:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (21:16-21:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (418:5-418:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (123:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (454:5-454:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (131:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (132:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (284:5-284:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (137:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (316:5-316:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (171:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (352:5-352:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (227:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (388:5-388:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (307:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (423:5-423:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (308:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (459:5-459:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (318:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (283:5-283:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (332:11)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (315:5-315:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (342:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (351:5-351:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (75:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (387:5-387:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (78:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (422:5-422:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (169:9-169:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (458:5-458:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (225:9-225:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (7:5-7:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (174:9-174:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_ext (9:5-9:20)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (230:9-230:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: genome_dir (45:5-45:46)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (7:5-7:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_genome (460:5-460:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: czid_dedup_out_duplicate_clusters_csv (44:5-44:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_genome (44:5-44:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (122:9-122:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: human_bowtie2_genome (424:5-424:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (74:9-74:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: human_star_genome (389:5-389:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (168:9-168:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lzw_fa (313:5-313:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (224:9-224:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_input_fragments (8:5-8:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (123:9-123:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_subsample_fragments (353:5-353:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (119:9-119:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nucleotide_type (43:5-43:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (173:9-173:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: priceseq_fa (249:5-249:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (229:9-229:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (184:5-184:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (33:5-33:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (217:5-217:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (248:5-248:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (76:9-76:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (281:5-281:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (170:9-170:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (312:5-312:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (226:9-226:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (348:5-348:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (45:5-45:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (382:5-382:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastas (121:9-121:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (39:5-39:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastas (73:9-73:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (419:5-419:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_counts_with_dcr_json (39:5-39:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (455:5-455:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_deduped_m8 (37:5-37:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_hitsummary_tab (38:5-38:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: star_genome (42:5-42:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8 (36:5-36:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: subsampled_fa (383:5-383:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (35:5-35:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: subsampled_fa (456:5-456:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (166:9-166:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: trimmomatic_fastq (218:5-218:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (222:9-222:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unmapped_fastq (185:5-185:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (125:9-125:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: unmapped_human_fa (420:5-420:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_minimap2_index (78:9-78:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valid_input_fastq (385:5-385:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (165:9-165:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valid_input_fastq (41:5-41:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (221:9-221:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: validate_input_summary_json (384:5-384:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (172:9-172:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: validate_input_summary_json (40:5-40:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (228:9-228:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: adapter_fasta (498:5-498:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_args (75:9-75:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bowtie2_genome (500:5-500:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (126:9-126:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (491:5-491:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (171:9-171:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (493:5-493:18)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (227:9-227:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (494:5-494:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (79:9-79:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (495:5-495:20)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_counts_with_dcr_json (43:5-43:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_genome (501:5-501:164)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_deduped_m8 (41:5-41:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_genome (497:5-497:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_hitsummary_tab (42:5-42:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: human_bowtie2_genome (503:5-503:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_m8 (40:5-40:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: human_star_genome (502:5-502:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (124:9-124:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_input_fragments (504:5-504:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (77:9-77:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_subsample_fragments (505:5-505:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (120:9-120:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nucleotide_type (496:5-496:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (175:9-175:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (492:5-492:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (231:9-231:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: star_genome (499:5-499:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (34:5-34:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (726:9-726:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (773:9-773:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (72:9-72:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: all_sequences_to_align (550:9-550:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (167:9-167:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotated_merged_fa (889:9-889:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (223:9-223:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads (427:9-427:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (286:5-286:105)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads (483:9-483:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: alignment_scalability (293:5-293:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads_fa (515:9-515:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: czid_dedup_out_duplicate_clusters_csv (283:5-283:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads_fa (596:9-596:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (290:5-290:101)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_taxid_annot_fasta (924:9-924:48)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (302:5-302:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (1221:9-1221:44)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (300:5-300:79)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (1222:9-1222:41)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (296:5-296:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (1223:9-1223:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_prefix (304:5-304:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fasta (1056:9-1056:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (277:5-277:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (1142:9-1142:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_cluster_sizes_tsv (282:5-282:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (551:9-551:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_1_fa (279:5-279:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (597:9-597:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_2_fa (280:5-280:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1015:9-1015:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_merged_fa (281:5-281:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1095:9-1095:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_dir_suffix (288:5-288:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (720:9-720:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_version (284:5-284:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (767:9-767:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (285:5-285:90)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (970:9-970:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_genome_name (297:5-297:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (598:9-598:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_index (294:5-294:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1020:9-1020:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_rapsearch2_index (298:5-298:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1058:9-1058:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (289:5-289:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1102:9-1102:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (301:5-301:52)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1143:9-1143:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (299:5-299:94)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (114:9-114:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (295:5-295:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1181:9-1181:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (303:5-303:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1225:9-1225:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (278:5-278:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (171:9-171:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (287:5-287:97)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (203:9-203:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (291:5-291:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (266:9-266:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (292:5-292:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (302:9-302:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (109:14-109:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (333:9-333:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (117:6-117:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (391:9-391:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (120:16-120:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (428:9-428:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (154:14-154:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (485:9-485:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (163:6-163:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (516:9-516:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (165:14-165:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (53:9-53:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (169:14-169:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (558:9-558:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (175:16-175:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (603:9-603:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (209:14-209:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (647:9-647:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (219:6-219:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (683:9-683:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (221:14-221:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (728:9-728:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (225:14-225:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (775:9-775:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (231:16-231:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (815:9-815:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (264:14-264:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (859:9-859:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (278:12-278:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (893:9-893:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (286:10-286:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (8:9-8:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (295:11-295:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (925:9-925:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (298:11-298:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (975:9-975:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (299:12-299:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: guppy_basecaller_setting (331:9-331:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (301:12-301:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (111:9-111:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (303:12-303:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (170:9-170:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:6-31:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (200:9-200:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:12-34:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (264:9-264:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:10-36:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (301:9-301:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:10-37:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (330:9-330:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (383:10-383:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (426:9-426:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (384:10-384:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (52:9-52:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (387:11-387:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (7:9-7:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (389:10-389:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (811:9-811:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (390:10-390:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (1180:9-1180:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (391:10-391:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: library_type (112:9-112:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (392:10-392:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: library_type (201:9-201:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (394:11-394:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1014:9-1014:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1094:9-1094:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (40:10-40:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (725:9-725:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:10-41:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (772:9-772:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (42:10-42:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (892:9-892:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (43:10-43:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (969:9-969:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (6:12-6:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (600:9-600:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (70:6-70:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_minimap2_index (554:9-554:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (72:16-72:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (727:9-727:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (75:16-75:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (774:9-774:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (78:15-78:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_args (552:9-552:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (160:5-160:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap_host_db (113:9-113:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (208:5-208:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap_human_db (202:9-202:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (151:5-151:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: non_contig_reads_fa (514:9-514:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (156:5-156:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (1092:9-1092:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (198:5-198:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1013:9-1013:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (204:5-204:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1091:9-1091:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (47:5-47:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (813:9-813:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (52:5-52:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (891:9-891:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (148:5-148:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (682:9-682:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (153:5-153:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1012:9-1012:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (195:5-195:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1090:9-1090:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (201:5-201:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (858:9-858:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (44:5-44:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_top_m8 (765:9-765:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (49:5-49:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (1088:9-1088:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_m8 (340:5-340:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1087:9-1087:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_m8 (347:5-347:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1219:9-1219:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_m8 (385:5-385:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (812:9-812:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_m8 (392:5-392:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (890:9-890:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_top_m8 (345:5-345:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (968:9-968:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_top_m8 (352:5-352:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (1224:9-1224:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_top_m8 (390:5-390:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8 (646:9-646:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_top_m8 (397:5-397:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1086:9-1086:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_contig_summary_json (344:5-344:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1218:9-1218:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_contig_summary_json (351:5-351:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (857:9-857:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_contig_summary_json (389:5-389:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (967:9-967:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_contig_summary_json (396:5-396:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (1220:9-1220:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_hitsummary2_tab (342:5-342:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (718:9-718:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_hitsummary2_tab (349:5-349:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: polishing_iterations (332:9-332:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_hitsummary2_tab (387:5-387:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pre_alignment_fasta (856:9-856:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_hitsummary2_tab (394:5-394:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (555:9-555:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_reassigned_m8 (341:5-341:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_contig_sam (1057:9-1057:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_reassigned_m8 (348:5-348:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (1011:9-1011:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_reassigned_m8 (386:5-386:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (719:9-719:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_reassigned_m8 (393:5-393:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (766:9-766:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_nr_refseq_fasta (199:5-199:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (966:9-966:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_nr_refseq_fasta (205:5-205:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contig_tsv (390:9-390:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_nt_refseq_fasta (152:5-152:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contig_tsv (484:9-484:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_nt_refseq_fasta (157:5-157:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contigs_sam (389:9-389:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_m8 (346:5-346:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contigs_tsv (814:9-814:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_m8 (353:5-353:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (553:9-553:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_m8 (391:5-391:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (599:9-599:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_m8 (398:5-398:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (557:9-557:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_top_m8 (351:5-351:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (602:9-602:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_top_m8 (358:5-358:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: subsample_depth (265:9-265:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_top_m8 (396:5-396:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1017:9-1017:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_top_m8 (403:5-403:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1097:9-1097:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_contig_summary_json (350:5-350:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (722:9-722:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_contig_summary_json (357:5-357:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (769:9-769:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_contig_summary_json (395:5-395:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (972:9-972:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_contig_summary_json (402:5-402:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1016:9-1016:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_hitsummary2_tab (348:5-348:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1096:9-1096:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_hitsummary2_tab (355:5-355:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (721:9-721:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_hitsummary2_tab (393:5-393:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (768:9-768:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_hitsummary2_tab (400:5-400:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (971:9-971:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_reassigned_m8 (347:5-347:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1018:9-1018:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_reassigned_m8 (354:5-354:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1099:9-1099:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_reassigned_m8 (392:5-392:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (723:9-723:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_reassigned_m8 (399:5-399:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (770:9-770:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (150:5-150:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (973:9-973:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (155:5-155:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1019:9-1019:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (197:5-197:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1100:9-1100:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (203:5-203:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (724:9-724:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (46:5-46:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (771:9-771:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (51:5-51:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (974:9-974:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_annotated_merged_fa (383:5-383:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (1274:9-1274:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_annotated_merged_fa (390:5-390:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (1278:9-1278:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_gsnap_counts_with_dcr_json (343:5-343:53)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (1286:9-1286:43)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_gsnap_counts_with_dcr_json (350:5-350:53)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (1285:9-1285:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_gsnap_counts_with_dcr_json (388:5-388:53)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (1271:9-1271:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_gsnap_counts_with_dcr_json (395:5-395:53)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (1254:9-1254:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_rapsearch2_counts_with_dcr_json (349:5-349:58)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: guppy_basecaller_setting (1261:9-1261:48)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_rapsearch2_counts_with_dcr_json (356:5-356:58)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_fastq (1258:9-1258:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_rapsearch2_counts_with_dcr_json (394:5-394:58)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: library_type (1260:9-1260:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_rapsearch2_counts_with_dcr_json (401:5-401:58)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (1273:9-1273:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_taxid_annot_mapped_only_fasta (428:5-428:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (1277:9-1277:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_taxid_annot_mapped_only_fasta (435:5-435:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (1282:9-1282:61)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_unidentified_fa (384:5-384:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (1281:9-1281:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_unidentified_fa (391:5-391:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (1270:9-1270:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (149:5-149:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (1283:9-1283:41)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (154:5-154:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_host_db (1265:9-1265:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (196:5-196:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_human_db (1266:9-1266:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (202:5-202:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (1279:9-1279:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (45:5-45:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: polishing_iterations (1268:9-1268:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (50:5-50:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (1256:9-1256:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_sizes_tsv (243:5-243:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: subsample_depth (1263:9-1263:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_sizes_tsv (250:5-250:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (1275:9-1275:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (283:5-283:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_whitelist (1276:9-1276:113)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (290:5-290:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (1288:9-1288:47)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: czid_dedup_out_duplicate_clusters_csv (352:5-352:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (1289:9-1289:44)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: czid_dedup_out_duplicate_clusters_csv (359:5-359:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_chunk (31:9-31:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (156:5-156:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (32:9-32:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (162:5-162:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: extra_args (30:9-30:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (247:5-247:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: query_0 (28:9-28:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (254:5-254:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: query_1 (29:9-29:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (108:5-108:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: db_chunk (8:9-8:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (113:5-113:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (9:9-9:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (142:5-142:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: extra_args (7:9-7:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (147:5-147:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: query_0 (5:9-5:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (189:5-189:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: query_1 (6:9-6:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (195:5-195:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (307:1-307:4)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (234:5-234:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W001::Style/Low] trailing space (53:139)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (241:5-241:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession_ids (115:9-115:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (281:5-281:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: clusters_directory (274:9-274:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (288:5-288:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cut_height (245:9-245:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (309:5-309:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: distances (327:9-327:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (316:5-316:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (120:9-120:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (337:5-337:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (190:9-190:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (344:5-344:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (210:9-210:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (381:5-381:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (247:9-247:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (388:5-388:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (277:9-277:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (426:5-426:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (329:9-329:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (42:5-42:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (352:9-352:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (433:5-433:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (375:9-375:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (47:5-47:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (397:9-397:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: newick (373:9-373:20)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (74:5-74:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_loc_db (119:9-119:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (79:5-79:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_s3_path (118:9-118:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (153:5-153:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (117:9-117:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (158:5-158:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_s3_path (116:9-116:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (200:5-200:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_accession_ids (396:9-396:46)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (206:5-206:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_taxon_id (188:9-188:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (353:5-353:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_and_reference_fastas (208:9-208:48)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (360:5-360:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (189:9-189:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (8:5-8:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (246:9-246:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_counts_with_dcr_json (147:5-147:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (328:9-328:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_counts_with_dcr_json (152:5-152:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (351:9-351:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_counts_with_dcr_json (79:5-79:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (374:9-374:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_counts_with_dcr_json (84:5-84:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ska_align_p (276:9-276:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_deduped_m8 (145:5-145:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ska_distances (244:9-244:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_deduped_m8 (150:5-150:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ska_hashes (275:9-275:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_deduped_m8 (77:5-77:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: superkingdom_name (209:9-209:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_deduped_m8 (82:5-82:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: variants (350:9-350:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_hitsummary_tab (146:5-146:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: additional_reference_accession_ids (19:9-19:62)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_hitsummary_tab (151:5-151:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cut_height (26:9-26:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_hitsummary_tab (78:5-78:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (28:9-28:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_hitsummary_tab (83:5-83:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_loc_db (24:9-24:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_m8 (144:5-144:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_s3_path (23:9-23:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_m8 (149:5-149:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (22:9-22:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_m8 (76:5-76:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_s3_path (21:9-21:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_m8 (81:5-81:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_taxon_id (14:9-14:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (339:5-339:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (31:9-31:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (346:5-346:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: samples (13:9-13:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (7:5-7:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ska_align_p (27:9-27:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (311:5-311:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: superkingdom_name (16:9-16:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (318:5-318:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (162:5-162:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (114:5-114:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (163:5-163:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (119:5-119:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (164:5-164:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (154:5-154:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (121:5-121:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (159:5-159:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (157:5-157:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (201:5-201:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (193:5-193:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (207:5-207:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (36:5-36:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (245:5-245:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (252:5-252:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (76:5-76:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (397:5-397:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (197:5-197:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (404:5-404:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (123:5-123:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (82:5-82:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (195:5-195:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (87:5-87:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_ext (124:5-124:20)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_contig_length (9:5-9:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8_gsnap_deduped_m8 (165:5-165:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (242:5-242:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8_gsnap_deduped_m8 (78:5-78:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (249:5-249:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (10:5-10:20)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_db (116:5-116:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nonhost_fasta_refined_taxid_annot_fasta (196:5-196:49)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_db (121:5-121:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_db (92:5-92:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hitsummary2_tab (241:5-241:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (166:5-166:20)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hitsummary2_tab (248:5-248:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (93:5-93:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_loc_db (115:5-115:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_blast_top_m8 (161:5-161:45)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_loc_db (120:5-120:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_hitsummary2_tab (160:5-160:48)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (240:5-240:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_reassigned_m8 (159:5-159:46)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (247:5-247:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: resist_genome_bed (126:5-126:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (239:5-239:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: resist_genome_db (125:5-125:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (246:5-246:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (122:5-122:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_db (80:5-80:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (158:5-158:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_db (85:5-85:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (194:5-194:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hitsummary2_tab (238:5-238:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (37:5-37:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hitsummary2_tab (245:5-245:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (81:5-81:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (77:5-77:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (86:5-86:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_fasta (38:5-38:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8 (237:5-237:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_family_nr_fasta (89:5-89:44)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8 (244:5-244:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_family_nt_fasta (87:5-87:44)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_counts_with_dcr_json (113:5-113:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_genus_nr_fasta (85:5-85:43)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_counts_with_dcr_json (118:5-118:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_genus_nt_fasta (83:5-83:43)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_counts_with_dcr_json (194:5-194:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_nr_fasta (81:5-81:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_counts_with_dcr_json (200:5-200:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_nt_fasta (79:5-79:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_deduped_m8 (111:5-111:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_fasta_in_annotated_merged_fa (7:5-7:44)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_deduped_m8 (116:5-116:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_fasta_in_gsnap_hitsummary_tab (8:5-8:45)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_deduped_m8 (192:5-192:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_fasta_in_rapsearch2_hitsummary_tab (9:5-9:50)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_deduped_m8 (198:5-198:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_combined_json (91:5-91:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_hitsummary_tab (112:5-112:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_family_nr_json (90:5-90:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_hitsummary_tab (117:5-117:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_family_nt_json (88:5-88:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_hitsummary_tab (193:5-193:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_genus_nr_json (86:5-86:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_hitsummary_tab (199:5-199:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_genus_nt_json (84:5-84:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_m8 (110:5-110:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_nr_json (82:5-82:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_m8 (115:5-115:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_nt_json (80:5-80:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_m8 (191:5-191:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (198:5-198:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_m8 (197:5-197:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_coverage_json (234:5-234:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (109:5-109:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_stats_json (235:5-235:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (114:5-114:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contigs_fasta (236:5-236:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (143:5-143:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (225:5-225:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (148:5-148:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_clusters_csv (240:5-240:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (190:5-190:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (237:5-237:18)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (196:5-196:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (238:5-238:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (235:5-235:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (241:5-241:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (242:5-242:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_m8_gsnap_deduped_m8 (230:5-230:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (282:5-282:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (245:5-245:90)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (289:5-289:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nonhost_fasta_refined_taxid_annot_fasta (239:5-239:49)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (310:5-310:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_db (242:5-242:76)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (317:5-317:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (244:5-244:89)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (338:5-338:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (243:5-243:87)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (345:5-345:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_blast_top_m8 (233:5-233:45)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (382:5-382:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_hitsummary2_tab (232:5-232:48)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (389:5-389:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_reassigned_m8 (231:5-231:46)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (427:5-427:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_bed (247:5-247:83)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (434:5-434:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_db (246:5-246:80)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (43:5-43:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (226:5-226:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (48:5-48:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_annotated_merged_fa (227:5-227:44)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_gsnap_hitsummary_tab (228:5-228:45)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (75:5-75:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_rapsearch2_hitsummary_tab (229:5-229:50)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (80:5-80:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (248:5-248:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (155:5-155:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: adapter_fasta (351:5-351:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (161:5-161:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (868:5-868:13)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (202:5-202:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_ercc_filtered1_fastq (349:5-349:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (209:5-209:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_ercc_filtered2_fastq (350:5-350:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (246:5-246:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_host_filtered1_fastq (626:5-626:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (253:5-253:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_host_filtered2_fastq (627:5-627:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (157:5-157:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_human_filtered1_fastq (795:5-795:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (163:5-163:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_human_filtered2_fastq (796:5-796:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (249:5-249:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_options (259:5-259:54)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (256:5-256:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_options (543:5-543:54)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (158:5-158:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_options (724:5-724:54)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (164:5-164:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (262:5-262:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (203:5-203:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (359:5-359:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (210:5-210:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (428:5-428:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (250:5-250:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (546:5-546:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (257:5-257:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (634:5-634:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (494:5-494:131)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (727:5-727:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: czid_dedup_out_duplicate_clusters_csv (480:5-480:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (803:5-803:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: czid_dedup_out_duplicate_clusters_csv (487:5-487:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup1_fastq (947:5-947:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (488:5-488:101)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup2_fastq (948:5-948:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (496:5-496:101)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (220:5-220:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (466:5-466:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (261:5-261:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (473:5-473:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (358:5-358:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_cluster_sizes_tsv (479:5-479:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (427:5-427:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_cluster_sizes_tsv (486:5-486:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (545:5-545:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_counts_with_dcr_json (474:5-474:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (633:5-633:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_counts_with_dcr_json (481:5-481:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (726:5-726:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_deduped_m8 (472:5-472:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (802:5-802:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_deduped_m8 (479:5-479:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (869:5-869:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_hitsummary_tab (473:5-473:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (913:5-913:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_hitsummary_tab (480:5-480:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (952:5-952:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_m8 (471:5-471:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (949:5-949:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_m8 (478:5-478:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ercc_index_tar (258:5-258:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_1_fa (468:5-468:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp1_fastq (419:5-419:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_1_fa (475:5-475:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp1_fastq (538:5-538:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_2_fa (469:5-469:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp2_fastq (420:5-420:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_2_fa (476:5-476:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp2_fastq (539:5-539:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_merged_fa (470:5-470:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp_options (354:5-356:82)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_merged_fa (477:5-477:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_ext (216:5-216:20)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_version (481:5-481:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_filtered1_fastq (911:5-911:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_version (488:5-488:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_filtered2_fastq (912:5-912:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (486:5-486:90)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_host_filtered1_fastq (719:5-719:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (493:5-493:90)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_host_filtered2_fastq (720:5-720:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_contig_length (491:5-491:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_options (631:5-631:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_contig_length (499:5-499:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_options (800:5-800:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_db (484:5-484:76)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (542:5-542:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_db (491:5-491:76)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (630:5-630:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_loc_db (485:5-485:87)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (723:5-723:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_loc_db (492:5-492:87)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (799:5-799:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_db (482:5-482:76)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kallisto_idx (421:5-421:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_db (489:5-489:76)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kallisto_options (425:5-425:54)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (483:5-483:87)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_input_fragments (218:5-218:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (490:5-490:87)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_subsample_fragments (950:5-950:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_counts_with_dcr_json (478:5-478:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads1_fastq (214:5-214:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_counts_with_dcr_json (485:5-485:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads2_fastq (215:5-215:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_deduped_m8 (476:5-476:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (221:5-221:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_deduped_m8 (483:5-483:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (914:5-914:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_hitsummary_tab (477:5-477:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (953:5-953:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_hitsummary_tab (484:5-484:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valid_input1_fastq (254:5-254:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_m8 (475:5-475:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valid_input2_fastq (255:5-255:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_m8 (482:5-482:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: adapter_fasta (14:5-14:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (467:5-467:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bowtie2_index_tar (17:5-17:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (474:5-474:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cpu (32:5-32:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (487:5-487:97)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (33:5-33:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (495:5-495:97)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ercc_index_tar (27:5-27:117)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (489:5-489:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (10:5-10:18)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (497:5-497:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (11:5-11:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (490:5-490:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (36:5-36:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (498:5-498:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gtf_gz (22:5-22:17)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (111:6-111:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_index_tar (18:5-18:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (114:12-114:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_genome (16:5-16:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (115:10-115:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: human_bowtie2_index_tar (24:5-24:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (116:10-116:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: human_hisat2_index_tar (25:5-25:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (117:10-117:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: kallisto_idx (19:5-19:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (118:10-118:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_input_fragments (29:5-29:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (145:6-145:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_subsample_fragments (30:5-30:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (148:12-148:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nucleotide_type (12:5-12:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (149:10-149:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (37:5-37:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (150:10-150:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (19:9-19:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (160:10-160:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (18:9-18:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (180:10-180:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (14:9-14:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (181:10-181:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (15:9-15:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (182:10-182:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (16:9-16:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (185:10-185:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (17:9-17:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (193:6-193:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: non_host_gsnap_genome_name (20:9-20:53)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (196:12-196:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (21:9-21:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (197:10-197:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (123:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (198:10-198:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (131:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (199:10-199:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (132:48)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (200:10-200:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (137:18)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (208:10-208:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (171:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (226:10-226:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (227:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (227:10-227:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (307:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (228:10-228:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (308:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (229:10-229:58)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (318:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (230:10-230:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (332:11)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (231:10-231:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (342:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (239:6-239:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (75:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (242:12-242:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (78:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (244:10-244:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (169:9-169:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (245:10-245:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (225:9-225:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (247:10-247:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (174:9-174:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (248:10-248:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (230:9-230:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (275:10-275:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (7:5-7:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (276:10-276:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: czid_dedup_out_duplicate_clusters_csv (44:5-44:47)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (286:6-286:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (122:9-122:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (289:12-289:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (74:9-74:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (314:6-314:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (168:9-168:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (317:12-317:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (224:9-224:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (342:6-342:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (123:9-123:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (345:12-345:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (119:9-119:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (347:10-347:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (173:9-173:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (348:10-348:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (229:9-229:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (349:10-349:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (33:5-33:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (352:10-352:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (353:10-353:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (76:9-76:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (354:10-354:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (170:9-170:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (355:10-355:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (226:9-226:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (356:10-356:58)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (45:5-45:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (357:10-357:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastas (121:9-121:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (358:10-358:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastas (73:9-73:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (386:6-386:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_counts_with_dcr_json (39:5-39:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (389:12-389:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_deduped_m8 (37:5-37:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (392:10-392:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_hitsummary_tab (38:5-38:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (393:10-393:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8 (36:5-36:18)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (394:10-394:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (35:5-35:48)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (397:10-397:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (166:9-166:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (398:10-398:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (222:9-222:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (399:10-399:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (125:9-125:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_minimap2_index (78:9-78:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (400:10-400:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (165:9-165:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (401:10-401:58)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (221:9-221:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (402:10-402:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (172:9-172:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (403:10-403:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (228:9-228:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (431:6-431:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_args (75:9-75:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (434:12-434:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (126:9-126:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (45:6-45:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (171:9-171:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (474:12-474:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (227:9-227:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (478:10-478:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (79:9-79:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (479:10-479:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_counts_with_dcr_json (43:5-43:41)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (482:10-482:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_deduped_m8 (41:5-41:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (483:10-483:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_hitsummary_tab (42:5-42:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (484:10-484:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_m8 (40:5-40:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (485:10-485:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (124:9-124:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (48:12-48:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (77:9-77:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (494:10-494:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (120:9-120:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (695:11-695:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (175:9-175:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (696:10-696:51)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (231:9-231:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (697:10-697:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (34:5-34:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (698:10-698:58)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (6:12-6:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (72:9-72:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (701:10-701:55)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (167:9-167:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (703:10-703:61)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (223:9-223:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (704:10-704:66)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (286:5-286:105)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (705:10-705:68)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: alignment_scalability (293:5-293:42)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (706:10-706:81)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: czid_dedup_out_duplicate_clusters_csv (283:5-283:47)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (707:10-707:72)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (290:5-290:101)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (708:10-708:65)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (302:5-302:42)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (709:11-709:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (300:5-300:79)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (77:6-77:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (296:5-296:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (80:12-80:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_prefix (304:5-304:41)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (81:10-81:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (277:5-277:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (82:10-82:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_cluster_sizes_tsv (282:5-282:37)" +document = "stjudecloud/workflows:data_structures/flag_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (124:10-124:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_1_fa (279:5-279:43)" +document = "stjudecloud/workflows:data_structures/flag_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (71:6-71:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_2_fa (280:5-280:44)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: sample_id (17:9-17:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_merged_fa (281:5-281:49)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (120:9-120:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_dir_suffix (288:5-288:44)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (28:9-28:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_version (284:5-284:40)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_gb (118:9-118:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (285:5-285:90)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_gb (26:9-26:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_genome_name (297:5-297:36)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: modify_disk_size_gb (119:9-119:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_index (294:5-294:28)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: modify_disk_size_gb (27:9-27:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_rapsearch2_index (298:5-298:33)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ncpu (117:9-117:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (289:5-289:29)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ncpu (25:9-25:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (301:5-301:52)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_all_cores (116:9-116:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (299:5-299:94)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_all_cores (24:9-24:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (295:5-295:33)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:17-119:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (303:5-303:37)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (120:17-120:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (278:5-278:21)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (82:14-82:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (287:5-287:97)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (83:14-83:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (291:5-291:43)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (87:14-87:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (292:5-292:40)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (141:11-141:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (151:5-151:36)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (142:11-142:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (198:5-198:36)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (151:12-151:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (47:5-47:36)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (152:12-152:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (148:5-148:32)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (168:14-168:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (195:5-195:32)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (169:15-169:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (44:5-44:32)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (73:11-73:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_m8 (340:5-340:33)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (74:11-74:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_m8 (385:5-385:33)" +document = "stjudecloud/workflows:tools/kraken2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (349:11-349:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_top_m8 (345:5-345:37)" +document = "stjudecloud/workflows:tools/kraken2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (350:11-350:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_top_m8 (390:5-390:37)" +document = "stjudecloud/workflows:tools/librarian.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:11-30:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_contig_summary_json (344:5-344:44)" +document = "stjudecloud/workflows:tools/md5sum.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:14-38:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_contig_summary_json (389:5-389:44)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (691:9-691:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_hitsummary2_tab (342:5-342:40)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:15-119:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_hitsummary2_tab (387:5-387:40)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (325:14-325:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_reassigned_m8 (341:5-341:38)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (420:14-420:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_reassigned_m8 (386:5-386:38)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (481:14-481:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_nr_refseq_fasta (199:5-199:34)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (480:20-480:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_nt_refseq_fasta (152:5-152:34)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (481:19-481:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_m8 (346:5-346:38)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (487:19-487:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_m8 (391:5-391:38)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (493:19-493:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_top_m8 (351:5-351:42)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (499:19-499:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_top_m8 (396:5-396:42)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (505:19-505:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_contig_summary_json (350:5-350:49)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (511:30-511:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_contig_summary_json (395:5-395:49)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (512:28-512:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_hitsummary2_tab (348:5-348:45)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (513:27-513:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_hitsummary2_tab (393:5-393:45)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (514:24-514:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_reassigned_m8 (347:5-347:43)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (515:24-515:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_reassigned_m8 (392:5-392:43)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (516:24-516:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (150:5-150:34)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (517:16-517:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (197:5-197:34)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (518:16-518:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (46:5-46:34)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (519:16-519:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_annotated_merged_fa (383:5-383:46)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (520:16-520:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_gsnap_counts_with_dcr_json (343:5-343:53)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (521:16-521:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_gsnap_counts_with_dcr_json (388:5-388:53)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (522:16-522:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_rapsearch2_counts_with_dcr_json (349:5-349:58)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (523:16-523:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_rapsearch2_counts_with_dcr_json (394:5-394:58)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (524:16-524:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_taxid_annot_mapped_only_fasta (428:5-428:56)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (525:16-525:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_unidentified_fa (384:5-384:42)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (526:16-526:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (149:5-149:34)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (527:16-527:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (196:5-196:34)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (528:16-528:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (45:5-45:34)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (529:16-529:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_sizes_tsv (243:5-243:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (530:16-530:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (283:5-283:34)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (531:16-531:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: czid_dedup_out_duplicate_clusters_csv (352:5-352:47)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (532:16-532:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (156:5-156:25)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (533:16-533:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (247:5-247:25)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (534:16-534:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (108:5-108:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (535:16-535:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (142:5-142:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (537:15-537:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (189:5-189:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (538:15-538:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (234:5-234:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (539:15-539:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (281:5-281:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (540:15-540:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (309:5-309:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (541:15-541:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (337:5-337:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (542:15-542:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (381:5-381:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (543:15-543:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (426:5-426:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (544:15-544:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (42:5-42:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (545:13-545:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (546:13-546:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (74:5-74:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (547:13-547:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (153:5-153:37)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (548:13-548:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (200:5-200:37)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (549:13-549:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (353:5-353:37)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (550:13-550:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (8:5-8:37)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (551:13-551:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_counts_with_dcr_json (147:5-147:46)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (552:13-552:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_counts_with_dcr_json (79:5-79:46)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (553:13-553:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_deduped_m8 (145:5-145:36)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (554:13-554:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_deduped_m8 (77:5-77:36)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (555:13-555:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_hitsummary_tab (146:5-146:40)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (556:13-556:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_hitsummary_tab (78:5-78:40)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (557:13-557:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_m8 (144:5-144:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (558:13-558:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_m8 (76:5-76:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (559:13-559:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (339:5-339:48)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (55:16-55:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (7:5-7:48)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (560:13-560:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (311:5-311:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (561:13-561:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (114:5-114:20)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (562:13-562:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (154:5-154:20)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (563:13-563:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (201:5-201:20)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (564:13-564:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (245:5-245:20)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (565:13-565:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (397:5-397:20)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (566:13-566:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (82:5-82:20)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (567:13-567:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_contig_length (9:5-9:26)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (568:13-568:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (242:5-242:32)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (569:13-569:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_db (116:5-116:17)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (56:16-56:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hitsummary2_tab (241:5-241:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (570:13-570:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_loc_db (115:5-115:19)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (571:13-571:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (240:5-240:15)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (572:13-572:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (239:5-239:32)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (573:13-573:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_db (80:5-80:17)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (574:13-574:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hitsummary2_tab (238:5-238:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (575:13-575:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (81:5-81:19)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (576:13-576:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8 (237:5-237:15)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (577:13-577:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_counts_with_dcr_json (113:5-113:56)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (578:13-578:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_counts_with_dcr_json (194:5-194:56)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (579:13-579:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_deduped_m8 (111:5-111:46)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (57:16-57:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_deduped_m8 (192:5-192:46)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (580:13-580:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_hitsummary_tab (112:5-112:50)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (581:13-581:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_hitsummary_tab (193:5-193:50)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (582:13-582:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_m8 (110:5-110:38)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (583:13-583:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_m8 (191:5-191:38)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (584:13-584:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (109:5-109:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (585:13-585:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (143:5-143:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (586:13-586:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (190:5-190:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (587:13-587:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (235:5-235:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (588:13-588:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (282:5-282:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (589:13-589:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (310:5-310:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (58:16-58:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (338:5-338:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (590:13-590:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (382:5-382:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (591:13-591:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (427:5-427:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (592:13-592:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (43:5-43:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (593:13-593:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (594:13-594:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (75:5-75:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (595:13-595:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (155:5-155:25)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (596:13-596:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (202:5-202:25)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (597:13-597:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (246:5-246:25)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (598:13-598:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (157:5-157:36)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (599:13-599:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (249:5-249:36)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (59:16-59:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (158:5-158:32)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (600:13-600:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (203:5-203:32)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (601:13-601:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (250:5-250:32)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (602:13-602:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: czid_dedup_out_duplicate_clusters_csv (480:5-480:47)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (603:13-603:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (488:5-488:101)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (604:13-604:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (466:5-466:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (60:16-60:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_cluster_sizes_tsv (479:5-479:37)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (62:13-62:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_counts_with_dcr_json (474:5-474:46)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (63:13-63:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_deduped_m8 (472:5-472:36)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (64:13-64:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_hitsummary_tab (473:5-473:40)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (65:13-65:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_m8 (471:5-471:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (66:13-66:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_1_fa (468:5-468:43)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (818:9-818:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_2_fa (469:5-469:44)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (819:9-819:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_merged_fa (470:5-470:49)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (820:9-820:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_version (481:5-481:40)" +document = "stjudecloud/workflows:tools/util.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: multiqc_tar_gz (692:9-692:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (486:5-486:90)" +document = "stjudecloud/workflows:tools/util.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outfile_name (693:9-693:95)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_contig_length (491:5-491:32)" +document = "stjudecloud/workflows:tools/util.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:17-26:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_db (484:5-484:76)" +document = "stjudecloud/workflows:tools/util.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (415:14-415:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_loc_db (485:5-485:87)" +document = "stjudecloud/workflows:workflows/general/bam-to-fastqs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (51:21-51:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_db (482:5-482:76)" +document = "stjudecloud/workflows:workflows/general/bam-to-fastqs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (52:22-52:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (483:5-483:87)" +document = "stjudecloud/workflows:workflows/qc/quality-check-standard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (572:11-572:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_counts_with_dcr_json (478:5-478:56)" +document = "stjudecloud/workflows:workflows/reference/bwa-db-build.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:17-28:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_deduped_m8 (476:5-476:46)" +document = "stjudecloud/workflows:workflows/reference/make-qc-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (127:14-127:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_hitsummary_tab (477:5-477:50)" +document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:17-35:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_m8 (475:5-475:38)" +document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:17-36:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (467:5-467:21)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (182:12-182:14)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (487:5-487:97)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (183:13-183:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (489:5-489:43)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (184:13-184:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (490:5-490:40)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (185:13-185:15)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W003::Completeness/Medium] extraneous parameter meta within task: sample_id (17:9-17:18)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (186:13-186:15)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (120:9-120:28)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (187:13-187:15)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (28:9-28:28)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (188:13-188:15)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_gb (118:9-118:27)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (189:13-189:15)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_gb (26:9-26:27)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (190:13-190:15)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: modify_disk_size_gb (119:9-119:36)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (191:10-191:12)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: modify_disk_size_gb (27:9-27:36)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (192:13-192:15)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ncpu (117:9-117:21)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (193:13-193:15)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ncpu (25:9-25:21)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (194:13-194:15)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_all_cores (116:9-116:38)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (195:13-195:15)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_all_cores (24:9-24:38)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (198:6-198:25)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/picard.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (691:9-691:46)" +document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cellranger11 (90:9-90:29)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/qualimap.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_retries (112:9-112:28)" +document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (94:9-94:30)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/qualimap.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_gb (110:9-110:27)" +document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gemcode (92:9-92:24)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/qualimap.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: modify_disk_size_gb (111:9-111:36)" +document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: longranger20 (91:9-91:29)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/qualimap.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ncpu (109:9-109:21)" +document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_gb (93:9-93:26)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/qualimap.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (107:9-107:46)" +document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (59:17-59:29)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/qualimap.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_all_cores (108:9-108:38)" +document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (60:17-60:29)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/util.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: multiqc_tar_gz (692:9-692:28)" +document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (83:21-83:27)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/util.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: outfile_name (693:9-693:95)" +document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (84:21-84:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cellranger11 (90:9-90:29)" +message = "[v1::W006::Naming/Low] identifier must be snake case (90:17-90:29)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: disk_size_gb (94:9-94:30)" +message = "[v1::W006::Naming/Low] identifier must be snake case (91:17-91:29)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gemcode (92:9-92:24)" +document = "stjudecloud/workflows:workflows/scrnaseq/scrnaseq-standard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (104:14-104:30)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: longranger20 (91:9-91:29)" +document = "stjudecloud/workflows:workflows/scrnaseq/scrnaseq-standard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (105:14-105:25)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/scrnaseq/10x-bam-to-fastqs.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: memory_gb (93:9-93:26)" +document = "stjudecloud/workflows:workflows/scrnaseq/scrnaseq-standard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (109:14-109:25)" [[concerns]] kind = "ParseError"