Linting: linting a pipeline also lints the installed subworkflows

CHANGELOG.md

@@ -15,6 +15,7 @@
 
 ### Linting
 
+- linting a pipeline also lints the installed subworkflows ([#2677](https://github.com/nf-core/tools/pull/2677))
 - environment.yml name must be lowercase ([#2676](https://github.com/nf-core/tools/pull/2676))
 
 ### Modules

nf_core/__main__.py

@@ -600,7 +600,7 @@ def lint(
 
     # Run the lint tests!
     try:
-        lint_obj, module_lint_obj = run_linting(
+        lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting(
             dir,
             release,
             fix,
@@ -613,7 +613,10 @@ def lint(
             json,
             ctx.obj["hide_progress"],
         )
-        if len(lint_obj.failed) + len(module_lint_obj.failed) > 0:
+        swf_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:
             sys.exit(1)
     except AssertionError as e:
         log.critical(e)

nf_core/lint/__init__.py

@@ -20,6 +20,7 @@
 
 import nf_core.lint_utils
 import nf_core.modules.lint
+import nf_core.subworkflows.lint
 import nf_core.utils
 from nf_core import __version__
 from nf_core.lint_utils import console
@@ -53,6 +54,8 @@ def run_linting(
 
     Returns:
         An object of type :class:`PipelineLint` that contains all the linting results.
+        An object of type :class:`ComponentLint` that contains all the linting results for the modules.
+        An object of type :class:`ComponentLint` that contains all the linting results for the subworkflows.
     """
 
     # Verify that the requested tests exist
@@ -87,6 +90,11 @@ def run_linting(
 
     # 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()
@@ -98,10 +106,19 @@ def run_linting(
         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 = ("module_changes", "module_version")
+        subworkflow_lint_tests = ("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 modules linting test
     module_lint_obj.set_up_pipeline_files()
@@ -119,11 +136,19 @@ def run_linting(
         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)
-    nf_core.lint_utils.print_joint_summary(lint_obj, module_lint_obj)
+    if subworkflow_lint_obj is not None:
+        subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
+    nf_core.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj)
     nf_core.lint_utils.print_fixes(lint_obj)
 
     # Save results to Markdown file
@@ -142,7 +167,7 @@ def run_linting(
         if release_mode:
             log.info("Reminder: Lint tests were run in --release mode.")
 
-    return lint_obj, module_lint_obj
+    return lint_obj, module_lint_obj, subworkflow_lint_obj
 
 
 class PipelineLint(nf_core.utils.Pipeline):

nf_core/lint_utils.py

@@ -16,13 +16,20 @@
 console = Console(force_terminal=nf_core.utils.rich_force_colors())
 
 
-def print_joint_summary(lint_obj, module_lint_obj):
-    """Print a joint summary of the general pipe lint tests and the module lint tests"""
-    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed)
+def print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj):
+    """Print a joint summary of the general pipe lint tests and the module and subworkflow lint tests"""
+    swf_passed = 0
+    swf_warned = 0
+    swf_failed = 0
+    if subworkflow_lint_obj is not None:
+        swf_passed = len(subworkflow_lint_obj.passed)
+        swf_warned = len(subworkflow_lint_obj.warned)
+        swf_failed = len(subworkflow_lint_obj.failed)
+    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed) + swf_passed
     nbr_ignored = len(lint_obj.ignored)
     nbr_fixed = len(lint_obj.fixed)
-    nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned)
-    nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed)
+    nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned) + swf_warned
+    nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed
 
     summary_colour = "red" if nbr_failed > 0 else "green"
     table = Table(box=rich.box.ROUNDED, style=summary_colour)

nf_core/pipeline-template/modules.json

@@ -7,17 +7,17 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
+                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
+                        "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
+                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     }
                 }