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

@@ -40,7 +40,6 @@ 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::
@@ -104,7 +103,6 @@ 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"]