allow linting a pipeline without nf-core components

nf_core/commands_pipelines.py

@@ -144,9 +144,12 @@ def pipelines_lint(
             ctx.obj["hide_progress"],
         )
         swf_failed = 0
+        module_failed = 0
         if subworkflow_lint_obj is not None:
             swf_failed = len(subworkflow_lint_obj.failed)
-        if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0:
+        if module_lint_obj is not None:
+            module_failed = len(module_lint_obj.failed)
+        if len(lint_obj.failed) + module_failed + swf_failed > 0:
             sys.exit(1)
     except AssertionError as e:
         log.critical(e)

nf_core/pipeline-template/main.nf

@@ -19,7 +19,6 @@
 
 include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
 {%- if modules %}
-{%- if modules %}
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 {%- if igenomes %}
@@ -58,10 +57,10 @@ workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
     {{ short_name|upper }} (
         samplesheet
     )
-{%- if multiqc or modules %}
+{%- if multiqc %}{%- if modules %}
     emit:
     multiqc_report = {{ short_name|upper }}.out.multiqc_report // channel: /path/to/multiqc_report.html
-{%- endif %}
+{%- endif %}{%- endif %}
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -74,7 +73,6 @@ workflow {
     main:
 
     {%- if modules %}
-    {%- modules %}
     //
     // SUBWORKFLOW: Run initialisation tasks
     //

nf_core/pipeline-template/nextflow_schema.json

@@ -57,6 +57,7 @@
                     "fa_icon": "fas fa-book",
                     "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
                 },
+                {%- if modules %}
                 "fasta": {
                     "type": "string",
                     "format": "file-path",
@@ -67,6 +68,7 @@
                     "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                     "fa_icon": "far fa-file-code"
                 },
+                {%- endif %}
                 "igenomes_ignore": {
                     "type": "boolean",
                     "description": "Do not load the iGenomes reference config.",

nf_core/pipeline-template/workflows/pipeline.nf

@@ -24,9 +24,9 @@ workflow {{ short_name|upper }} {
     take:
     ch_samplesheet // channel: samplesheet read in from --input
 
+    {%- if modules %}
     main:
 
-    {%- if modules %}
     ch_versions = Channel.empty()
     {% if multiqc %}ch_multiqc_files = Channel.empty(){% endif %}
 

nf_core/pipelines/create/templatefeatures.yml

@@ -238,6 +238,33 @@ fastqc:
     The pipeline will include the FastQC module.
   nfcore_pipelines: True
   custom_pipelines: True
+modules:
+  skippable_paths:
+    - "conf/base.config"
+    - "conf/modules.config"
+    - "conf/modules.json"
+    - "modules"
+    - "subworkflows"
+  short_description: "Use nf-core components"
+  description: "Include all required files to use nf-core modules and subworkflows"
+  help_text: |
+    It is *recommended* to use this feature if you want to use modules and subworkflows in your pipeline.
+    This will add all required files to use nf-core components or any compatible components from private repos by using `nf-core modules` and `nf-core subworkflows` commands.
+  linting:
+    nfcore_components: False
+    modules_json: False
+    base_config: False
+    modules_config: False
+    files_exist:
+      - "conf/base.config"
+      - "conf/modules.config"
+      - "conf/modules.json"
+    nextflow_config:
+      - "process.cpus"
+      - "process.memory"
+      - "process.time"
+  nfcore_pipelines: False
+  custom_pipelines: True
 changelog:
   skippable_paths:
     - "CHANGELOG.md"
@@ -285,20 +312,6 @@ email:
       - ".prettierignore"
   nfcore_pipelines: False
   custom_pipelines: True
-modules:
-  skippable_paths:
-    - "conf/base.config"
-    - "conf/modules.config"
-    - "conf/modules.json"
-    - "modules"
-    - "subworkflows"
-  short_description: "Use nf-core components"
-  description: "Include all required files to use nf-core modules and subworkflows"
-  help_text: |
-    It is *recommended* to use this feature if you want to use modules and subworkflows in your pipeline.
-    This will add all required files to use nf-core components or any compatible components from private repos by using `nf-core modules` and `nf-core subworkflows` commands.
-  nfcore_pipelines: False
-  custom_pipelines: True
 adaptivecard:
   skippable_paths:
     - "assets/adaptivecard.json"

nf_core/pipelines/lint/__init__.py

@@ -149,6 +149,7 @@ def _get_all_lint_tests(release_mode):
             "base_config",
             "modules_config",
             "nfcore_yml",
+            "nfcore_components",
         ] + (["version_consistency"] if release_mode else [])
 
     def _load(self) -> bool:
@@ -543,7 +544,7 @@ def run_linting(
     md_fn=None,
     json_fn=None,
     hide_progress: bool = False,
-) -> Tuple[PipelineLint, ComponentLint, Union[ComponentLint, None]]:
+) -> Tuple[PipelineLint, Union[ComponentLint, None], Union[ComponentLint, None]]:
     """Runs all nf-core linting checks on a given Nextflow pipeline project
     in either `release` mode or `normal` mode (default). Returns an object
     of type :class:`PipelineLint` after finished.
@@ -588,41 +589,45 @@ def run_linting(
     lint_obj._load_lint_config()
     lint_obj.load_pipeline_config()
 
-    # Create the modules lint object
-    module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
-    # Create the subworkflows lint object
-    try:
-        subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, hide_progress=hide_progress)
-    except LookupError:
-        subworkflow_lint_obj = None
-
-    # Verify that the pipeline is correctly configured and has  a modules.json file
-    module_lint_obj.has_valid_directory()
-    module_lint_obj.has_modules_file()
-    # Run only the tests we want
-    if key:
-        # Select only the module lint tests
-        module_lint_tests = list(
-            set(key).intersection(set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)))
-        )
-        # Select only the subworkflow lint tests
-        subworkflow_lint_tests = list(
-            set(key).intersection(
-                set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True))
+    if "nfcore_components" in lint_obj.lint_config and not lint_obj.lint_config:
+        # Create the modules lint object
+        module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
+        # Create the subworkflows lint object
+        try:
+            subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, hide_progress=hide_progress)
+        except LookupError:
+            subworkflow_lint_obj = None
+
+        # Verify that the pipeline is correctly configured and has  a modules.json file
+        module_lint_obj.has_valid_directory()
+        module_lint_obj.has_modules_file()
+        # Run only the tests we want
+        if key:
+            # Select only the module lint tests
+            module_lint_tests = list(
+                set(key).intersection(set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)))
             )
-        )
+            # Select only the subworkflow lint tests
+            subworkflow_lint_tests = list(
+                set(key).intersection(
+                    set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True))
+                )
+            )
+        else:
+            # If no key is supplied, run the default modules tests
+            module_lint_tests = list(("module_changes", "module_version"))
+            subworkflow_lint_tests = list(("subworkflow_changes", "subworkflow_version"))
+        module_lint_obj.filter_tests_by_key(module_lint_tests)
+        if subworkflow_lint_obj is not None:
+            subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)
+
+        # Set up files for component linting test
+        module_lint_obj.set_up_pipeline_files()
+        if subworkflow_lint_obj is not None:
+            subworkflow_lint_obj.set_up_pipeline_files()
     else:
-        # If no key is supplied, run the default modules tests
-        module_lint_tests = list(("module_changes", "module_version"))
-        subworkflow_lint_tests = list(("subworkflow_changes", "subworkflow_version"))
-    module_lint_obj.filter_tests_by_key(module_lint_tests)
-    if subworkflow_lint_obj is not None:
-        subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)
-
-    # Set up files for component linting test
-    module_lint_obj.set_up_pipeline_files()
-    if subworkflow_lint_obj is not None:
-        subworkflow_lint_obj.set_up_pipeline_files()
+        module_lint_obj = None
+        subworkflow_lint_obj = None
 
     # Run the pipeline linting tests
     try:
@@ -632,24 +637,26 @@ def run_linting(
         log.info("Stopping tests...")
         return lint_obj, module_lint_obj, subworkflow_lint_obj
 
-    # Run the module lint tests
-    if len(module_lint_obj.all_local_components) > 0:
-        module_lint_obj.lint_modules(module_lint_obj.all_local_components, local=True)
-    if len(module_lint_obj.all_remote_components) > 0:
-        module_lint_obj.lint_modules(module_lint_obj.all_remote_components, local=False)
-    # Run the subworkflows lint tests
-    if subworkflow_lint_obj is not None:
-        if len(subworkflow_lint_obj.all_local_components) > 0:
-            subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_local_components, local=True)
-        if len(subworkflow_lint_obj.all_remote_components) > 0:
-            subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_remote_components, local=False)
+    if module_lint_obj is not None and subworkflow_lint_obj is not None:
+        # Run the module lint tests
+        if len(module_lint_obj.all_local_components) > 0:
+            module_lint_obj.lint_modules(module_lint_obj.all_local_components, local=True)
+        if len(module_lint_obj.all_remote_components) > 0:
+            module_lint_obj.lint_modules(module_lint_obj.all_remote_components, local=False)
+        # Run the subworkflows lint tests
+        if subworkflow_lint_obj is not None:
+            if len(subworkflow_lint_obj.all_local_components) > 0:
+                subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_local_components, local=True)
+            if len(subworkflow_lint_obj.all_remote_components) > 0:
+                subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_remote_components, local=False)
 
     # Print the results
     lint_obj._print_results(show_passed)
-    module_lint_obj._print_results(show_passed, sort_by=sort_by)
-    if subworkflow_lint_obj is not None:
-        subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
-    nf_core.pipelines.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj)
+    if module_lint_obj is not None and subworkflow_lint_obj is not None:
+        module_lint_obj._print_results(show_passed, sort_by=sort_by)
+        if subworkflow_lint_obj is not None:
+            subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
+        nf_core.pipelines.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj)
     nf_core.pipelines.lint_utils.print_fixes(lint_obj)
 
     # Save results to Markdown file