From 83ec5c7e61661f604e0b9b95d43f616c10a10464 Mon Sep 17 00:00:00 2001
From: darcy220606 <ananhamido@hotmail.com>
Date: Tue, 22 Aug 2023 11:28:16 +0200
Subject: [PATCH 1/4] stop prokka from renaming contigs by default
---
CHANGELOG.md | 11 +++++++++++
conf/modules.config | 3 +--
nextflow.config | 3 +--
nextflow_schema.json | 18 +++++-------------
4 files changed, 18 insertions(+), 17 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7fa76fc2..b4214bd2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,17 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## v1.1.4dev - [unreleased]
+
+### `Added`
+
+### `Fixed`
+- [###]() Added new parameter `annotation_prokka_renamecontigs` to allow prokka to retain the original contig headers/locus tag by default (fix by @darcy220606)
+
+### `Dependencies`
+
+### `Deprecated`
+
## v1.1.3 - [2023-08-11]
### `Added`
diff --git a/conf/modules.config b/conf/modules.config
index f5472ced..0a2fdbd5 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -65,8 +65,7 @@ process {
"--mincontiglen ${params.annotation_prokka_mincontiglen}",
"--evalue ${params.annotation_prokka_evalue}",
"--coverage ${params.annotation_prokka_coverage}",
- "--centre ${params.annotation_prokka_centre}",
- "--locustag ${params.annotation_prokka_locustag}",
+ params.annotation_prokka_renamecontigs ? "--locustag PROKKA --centre CENTER" : "--force" ,
params.annotation_prokka_singlemode ? '' : '--metagenome' ,
params.annotation_prokka_cdsrnaolap ? '--cdsrnaolap' : '',
params.annotation_prokka_rawproduct ? '--rawproduct' : '',
diff --git a/nextflow.config b/nextflow.config
index 95ffa0c1..a094f9ec 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -62,10 +62,9 @@ params {
annotation_prokka_mincontiglen = 1
annotation_prokka_evalue = 1E-06
annotation_prokka_coverage = 80
- annotation_prokka_centre = null
annotation_prokka_compliant = false
- annotation_prokka_locustag = 'PROKKA'
annotation_prokka_addgenes = false
+ annotation_prokka_renamecontigs = false
// Database downloading options
save_databases = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 93979e7d..c7f5d1d6 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -297,30 +297,22 @@
"help_text": "Activates [RNAmmer](https://services.healthtech.dtu.dk/service.php?RNAmmer-1.2) instead of the Prokka default [Barrnap](https://github.com/tseemann/barrnap) for rRNA prediction during the annotation process. RNAmmer classifies ribosomal RNA genes in genome sequences by using two levels of Hidden Markov Models. Barrnap uses the nhmmer tool that includes HMMER 3.1 for HMM searching in RNA:DNA style.\n\nFor more information please check Prokka [documentation](https://github.com/tseemann/prokka).\n\n> Modifies tool parameter(s):\n> - Prokka: `--rnammer`",
"fa_icon": "fas fa-adjust"
},
- "annotation_prokka_centre": {
- "type": "string",
- "description": "Sequencing centre ID.",
- "fa_icon": "fas fa-map-marker-alt",
- "help_text": "Add the sequencing center ID used in generating the raw sequences. This flag is typically requested in combination with the `--compliant` flag when contigs need to be renamed due to non-conforming contig headers. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--centre`"
- },
"annotation_prokka_compliant": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Force contig name to Genbank/ENA/DDJB naming rules.",
"help_text": "Force the contig headers to conform to the Genbank/ENA/DDJB contig header standards. This is activated in combination with `--centre [X]` when contig headers supplied by the user are non-conforming and therefore need to be renamed before Prokka can start annotation. This flag activates `--genes --mincontiglen 200`. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--compliant`"
},
- "annotation_prokka_locustag": {
- "type": "string",
- "default": "Prokka",
- "fa_icon": "fas fa-tags",
- "description": "Assign the locus tag for the contig header.",
- "help_text": "Assign a special name to the contig. This is used when a specific group of samples are run in a batch. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--locustag`"
- },
"annotation_prokka_addgenes": {
"type": "boolean",
"fa_icon": "fas fa-dna",
"description": "Add the gene features for each CDS hit.",
"help_text": "For every CDS annotated, this flag adds the gene that encodes for that CDS region. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--addgenes`"
+ },
+ "annotation_prokka_renamecontigs": {
+ "type": "boolean",
+ "help_text": "This parameter retains the original contig names by activating `PROKKA`'s `--force` flag. If this parameter is set to `true` it activates `PROKKA`'s flags `--locus-tag PROKKA --centre CENTER` so the locus tags (contig names) will be PROKKA_# and the center tag will be CENTER. \n\n> Modifies tool parameter(s):\n> - Prokka: `--locus-tag PROKKA --centre CENTER`\n> - Prokka: `--force`",
+ "description": "Renames contig names."
}
},
"fa_icon": "fas fa-tools",
From eaf43875557467cf5f3e34a448301cf8ad16e54f Mon Sep 17 00:00:00 2001
From: darcy220606 <ananhamido@hotmail.com>
Date: Tue, 22 Aug 2023 12:02:03 +0200
Subject: [PATCH 2/4] CHANGELOG prettier
---
CHANGELOG.md | 1 +
1 file changed, 1 insertion(+)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b4214bd2..a75dbb51 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Added`
### `Fixed`
+
- [###]() Added new parameter `annotation_prokka_renamecontigs` to allow prokka to retain the original contig headers/locus tag by default (fix by @darcy220606)
### `Dependencies`
From 628111b426ab3340d37e95505997d6b2b0409205 Mon Sep 17 00:00:00 2001
From: darcy220606 <ananhamido@hotmail.com>
Date: Wed, 23 Aug 2023 10:23:21 +0200
Subject: [PATCH 3/4] Fix new parameter
---
CHANGELOG.md | 2 +-
conf/modules.config | 2 +-
nextflow.config | 4 ++--
nextflow_schema.json | 6 +++---
4 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a75dbb51..f366a0ee 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Fixed`
-- [###]() Added new parameter `annotation_prokka_renamecontigs` to allow prokka to retain the original contig headers/locus tag by default (fix by @darcy220606)
+- [###]() Added new parameter `annotation_prokka_retaincontigheaders` to allow prokka to retain the original contig headers/locus tag. (by @darcy220606)
### `Dependencies`
diff --git a/conf/modules.config b/conf/modules.config
index 0a2fdbd5..c94e5324 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -65,7 +65,7 @@ process {
"--mincontiglen ${params.annotation_prokka_mincontiglen}",
"--evalue ${params.annotation_prokka_evalue}",
"--coverage ${params.annotation_prokka_coverage}",
- params.annotation_prokka_renamecontigs ? "--locustag PROKKA --centre CENTER" : "--force" ,
+ params.annotation_prokka_retaincontigheaders ? "--force" : "--locustag PROKKA --centre CENTER" ,
params.annotation_prokka_singlemode ? '' : '--metagenome' ,
params.annotation_prokka_cdsrnaolap ? '--cdsrnaolap' : '',
params.annotation_prokka_rawproduct ? '--rawproduct' : '',
diff --git a/nextflow.config b/nextflow.config
index a094f9ec..599de35c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -62,9 +62,9 @@ params {
annotation_prokka_mincontiglen = 1
annotation_prokka_evalue = 1E-06
annotation_prokka_coverage = 80
- annotation_prokka_compliant = false
+ annotation_prokka_compliant = true
annotation_prokka_addgenes = false
- annotation_prokka_renamecontigs = false
+ annotation_prokka_retaincontigheaders = false
// Database downloading options
save_databases = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index c7f5d1d6..56bef890 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -309,10 +309,10 @@
"description": "Add the gene features for each CDS hit.",
"help_text": "For every CDS annotated, this flag adds the gene that encodes for that CDS region. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--addgenes`"
},
- "annotation_prokka_renamecontigs": {
+ "annotation_prokka_retaincontigheaders": {
"type": "boolean",
- "help_text": "This parameter retains the original contig names by activating `PROKKA`'s `--force` flag. If this parameter is set to `true` it activates `PROKKA`'s flags `--locus-tag PROKKA --centre CENTER` so the locus tags (contig names) will be PROKKA_# and the center tag will be CENTER. \n\n> Modifies tool parameter(s):\n> - Prokka: `--locus-tag PROKKA --centre CENTER`\n> - Prokka: `--force`",
- "description": "Renames contig names."
+ "help_text": "This parameter allows prokka to retain the original contig names by activating `PROKKA`'s `--force` flag. If this parameter is set to `false` it activates `PROKKA`'s flags `--locus-tag PROKKA --centre CENTER` so the locus tags (contig names) will be PROKKA_# and the center tag will be CENTER. By default `PROKKA` changes contig headers to avoid errors that might rise due to long contig headers, so this must be turned on if the user has short contig names that should be retained by `PROKKA`. \n\n> Modifies tool parameter(s):\n> - Prokka: `--locus-tag PROKKA --centre CENTER`\n> - Prokka: `--force`",
+ "description": "Retains contig names."
}
},
"fa_icon": "fas fa-tools",
From c749b5eb66be56418fdc90e18d45d74b7fda0a99 Mon Sep 17 00:00:00 2001
From: darcy220606 <ananhamido@hotmail.com>
Date: Fri, 25 Aug 2023 09:38:14 +0200
Subject: [PATCH 4/4] Add review requests
---
CHANGELOG.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f366a0ee..231d9274 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Fixed`
-- [###]() Added new parameter `annotation_prokka_retaincontigheaders` to allow prokka to retain the original contig headers/locus tag. (by @darcy220606)
+- [#306](https://github.com/nf-core/funcscan/pull/306) Added new parameter `annotation_prokka_retaincontigheaders` to allow prokka to retain the original contig headers/locus tag. (by @darcy220606)
### `Dependencies`