Merge pull request #2736 from nf-core/rm_lib

Remove lib directory and replace it with granular utils_* subworkflows

.prettierignore

@@ -6,6 +6,7 @@ testing
 nf_core/module-template/meta.yml
 nf_core/module-template/tests/tags.yml
 nf_core/subworkflow-template/tests/tags.yml
+nf_core/pipeline-template/nextflow_schema.json
 # don't run on things handled by ruff
 *.py
 *.pyc

nf_core/create.py

@@ -292,7 +292,7 @@ def render_template(self):
  short_name = self.template_params["short_name"]
  rename_files = {
  "workflows/pipeline.nf": f"workflows/{short_name}.nf",
- "lib/WorkflowPipeline.groovy": f"lib/Workflow{short_name[0].upper()}{short_name[1:]}.groovy",
+ "subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf": f"subworkflows/local/utils_nfcore_{short_name}_pipeline/main.nf",
  }
 
  # Set the paths to skip according to customization

nf_core/lint/files_exist.py

@@ -52,9 +52,6 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
  docs/output.md
  docs/README.md
  docs/usage.md
- lib/NfcoreTemplate.groovy
- lib/Utils.groovy
- lib/WorkflowMain.groovy
  nextflow_schema.json
  nextflow.config
  README.md
@@ -69,7 +66,6 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
  conf/igenomes.config
  .github/workflows/awstest.yml
  .github/workflows/awsfulltest.yml
- lib/WorkflowPIPELINE.groovy
  pyproject.toml
 
  Files that *must not* be present, due to being renamed or removed in the template:
@@ -91,6 +87,11 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
  lib/Checks.groovy
  lib/Completion.groovy
  lib/Workflow.groovy
+ lib/WorkflowPIPELINE.groovy
+ lib/NfcoreTemplate.groovy
+ lib/Utils.groovy
+ lib/WorkflowMain.groovy
+
 
  Files that *should not* be present:
 
@@ -165,9 +166,6 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
  [Path("docs", "README.md")],
  [Path("docs", "README.md")],
  [Path("docs", "usage.md")],
- [Path("lib", "NfcoreTemplate.groovy")],
- [Path("lib", "Utils.groovy")],
- [Path("lib", "WorkflowMain.groovy")],
  ]
 
  files_warn = [
@@ -177,7 +175,6 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
  [Path("conf", "igenomes.config")],
  [Path(".github", "workflows", "awstest.yml")],
  [Path(".github", "workflows", "awsfulltest.yml")],
- [Path("lib", f"Workflow{short_name[0].upper()}{short_name[1:]}.groovy")],
  [Path("modules.json")],
  [Path("pyproject.toml")],
  ]
@@ -199,6 +196,10 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
  Path("lib", "Checks.groovy"),
  Path("lib", "Completion.groovy"),
  Path("lib", "Workflow.groovy"),
+ Path("lib", "Utils.groovy"),
+ Path("lib", "WorkflowMain.groovy"),
+ Path("lib", "NfcoreTemplate.groovy"),
+ Path("lib", f"Workflow{short_name[0].upper()}{short_name[1:]}.groovy"),
  ]
  files_warn_ifexists = [Path(".travis.yml")]
  files_fail_ifinconfig: List[Tuple[Path, Dict[str, str]]] = [

nf_core/lint/files_unchanged.py

@@ -41,7 +41,6 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]:
  docs/images/nf-core-PIPELINE_logo_light.png
  docs/images/nf-core-PIPELINE_logo_dark.png
  docs/README.md'
- lib/NfcoreTemplate.groovy
  ['LICENSE', 'LICENSE.md', 'LICENCE', 'LICENCE.md'], # NB: British / American spelling
 
  Files that can have additional content but must include the template contents::
@@ -105,7 +104,6 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]:
  [Path("docs", "images", f"nf-core-{short_name}_logo_light.png")],
  [Path("docs", "images", f"nf-core-{short_name}_logo_dark.png")],
  [Path("docs", "README.md")],
- [Path("lib", "NfcoreTemplate.groovy")],
  ]
  files_partial = [
  [Path(".gitignore"), Path(".prettierignore"), Path("pyproject.toml")],

nf_core/pipeline-template/.editorconfig

@@ -18,7 +18,12 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-indent_size = unset
+[/subworkflows/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
 
 [/assets/email*]
 indent_size = unset

nf_core/pipeline-template/assets/multiqc_config.yml

@@ -17,3 +17,5 @@ report_section_order:
  order: -1002
 
 export_plots: true
+
+disable_version_detection: true

nf_core/pipeline-template/assets/schema_input.json

@@ -10,25 +10,22 @@
  "sample": {
  "type": "string",
  "pattern": "^\\S+$",
- "errorMessage": "Sample name must be provided and cannot contain spaces"
+ "errorMessage": "Sample name must be provided and cannot contain spaces",
+ "meta": ["id"]
  },
  "fastq_1": {
  "type": "string",
+ "format": "file-path",
+ "exists": true,
  "pattern": "^\\S+\\.f(ast)?q\\.gz$",
  "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
  },
  "fastq_2": {
- "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
- "anyOf": [
- {
- "type": "string",
- "pattern": "^\\S+\\.f(ast)?q\\.gz$"
- },
- {
- "type": "string",
- "maxLength": 0
- }
- ]
+ "type": "string",
+ "format": "file-path",
+ "exists": true,
+ "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+ "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
  }
  },
  "required": ["sample", "fastq_1"]