Linting: linting a pipeline also lints the installed subworkflows

CHANGELOG.md

@@ -15,6 +15,8 @@
 
 ### Linting
 
+- linting a pipeline also lints the installed subworkflows ([#2677](https://github.com/nf-core/tools/pull/2677))
+
 ### Modules
 
 - Fix linting of a pipeline with patched custom module ([#2669](https://github.com/nf-core/tools/pull/2669))

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 +613,7 @@ def lint(
  json,
  ctx.obj["hide_progress"],
  )
- if len(lint_obj.failed) + len(module_lint_obj.failed) > 0:
+ if len(lint_obj.failed) + len(module_lint_obj.failed) + len(subworkflow_lint_obj.failed) > 0:
  sys.exit(1)
  except AssertionError as e:
  log.critical(e)

nf_core/components/lint/__init__.py

@@ -97,9 +97,7 @@ def __init__(
  )
  )
  if not self.all_remote_components:
- raise LookupError(
- f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline."
- )
+ log.warning(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.")
  local_component_dir = Path(self.dir, self.component_type, "local")
  self.all_local_components = []
  if local_component_dir.exists():

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 +90,8 @@ 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
+ subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, hide_progress=hide_progress)
 
  # Verify that the pipeline is correctly configured and has a modules.json file
  module_lint_obj.has_valid_directory()
@@ -98,10 +103,18 @@ 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)
+ 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 +132,17 @@ 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 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)
+ 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 +161,7 @@ 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 +16,13 @@
 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"""
+ nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed) + len(subworkflow_lint_obj.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) + len(subworkflow_lint_obj.warned)
+ nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed) + len(subworkflow_lint_obj.failed)
 
  summary_colour = "red" if nbr_failed > 0 else "green"
  table = Table(box=rich.box.ROUNDED, style=summary_colour)