Add command nf-core subworkflows lint

CHANGELOG.md

@@ -14,6 +14,8 @@
 
 ### Linting
 
+- Add new command `nf-core subworkflows lint` ([#2379](https://github.com/nf-core/tools/pull/2379))
+
 ### Modules
 
 ### Subworkflows

README.md

@@ -54,6 +54,7 @@ A python package with helper tools for the nf-core community.
   - [`subworkflows remove` - Remove a subworkflow from a pipeline](#remove-a-subworkflow-from-a-pipeline)
   - [`subworkflows create` - Create a subworkflow from the template](#create-a-new-subworkflow)
   - [`subworkflows create-test-yml` - Create the `test.yml` file for a subworkflow](#create-a-subworkflow-test-config-file)
+  - [`subworkflows lint` - Check a subworkflow against nf-core guidelines](#check-a-subworkflow-against-nf-core-guidelines)
   - [`subworkflows test` - Run the tests for a subworkflow](#run-the-tests-for-a-subworkflow-using-pytest)
 - [Citation](#citation)
 
@@ -1218,6 +1219,20 @@ extra_env:
 
 ![`nf-core subworkflows create-test-yml bam_stats_samtools --no-prompts --force`](docs/images/nf-core-subworkflows-create-test.svg)
 
+### Check a subworkflow against nf-core guidelines
+
+Run the `nf-core subworkflows lint` command to check subworkflows in the current working directory (a pipeline or a clone of nf-core/modules) against nf-core guidelines.
+
+Use the `--all` flag to run linting on all subworkflows found. Use `--dir <pipeline_dir>` to specify a different directory than the current working directory.
+
+<!-- RICH-CODEX
+working_dir: tmp/modules
+extra_env:
+  PROFILE: 'conda'
+-->
+
+![`nf-core subworkflows lint bam_stats_samtools`](docs/images/nf-core-subworkflows-lint.svg)
+
 ### Run the tests for a subworkflow using pytest
 
 To run unit tests of a subworkflow that you have installed or the test created by the command [`nf-core subworkflow create-test-yml`](#create-a-subworkflow-test-config-file), you can use `nf-core subworkflows test` command. This command runs the tests specified in `tests/subworkflows/<subworkflow_name>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).

docs/api/make_lint_md.py

@@ -5,6 +5,7 @@
 
 import nf_core.lint
 import nf_core.modules.lint
+import nf_core.subworkflows.lint
 
 
 def make_docs(docs_basedir, lint_tests, md_template):
@@ -55,3 +56,20 @@ def make_docs(docs_basedir, lint_tests, md_template):
 ```
 """,
 )
+
+# Create the subworkflows lint docs
+subworkflows_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "subworkflow_lint_tests")
+make_docs(
+    subworkflows_docs_basedir,
+    list(
+        set(nf_core.subworkflows.lint.SubworkflowLint.get_all_lint_tests(is_pipeline=True)).union(
+            nf_core.subworkflows.lint.SubworkflowLint.get_all_lint_tests(is_pipeline=False)
+        )
+    ),
+    """# {0}
+
+```{{eval-rst}}
+.. automethod:: nf_core.subworkflows.lint.SubworkflowLint.{0}
+```
+""",
+)

nf_core/__main__.py

@@ -912,8 +912,8 @@ def lint(
     Test modules within a pipeline or a clone of the
     nf-core/modules repository.
     """
+    from nf_core.components.lint import LintException
     from nf_core.modules import ModuleLint
-    from nf_core.modules.lint import ModuleLintException
 
     try:
         module_lint = ModuleLint(
@@ -938,7 +938,7 @@ def lint(
         )
         if len(module_lint.failed) > 0:
             sys.exit(1)
-    except ModuleLintException as e:
+    except LintException as e:
         log.error(e)
         sys.exit(1)
     except (UserWarning, LookupError) as e:
@@ -1170,6 +1170,76 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
         sys.exit(1)
 
 
+# nf-core subworkflows lint
+@subworkflows.command()
+@click.pass_context
+@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<pipeline/modules directory>")
+@click.option(
+    "-r",
+    "--registry",
+    type=str,
+    metavar="<registry>",
+    default=None,
+    help="Registry to use for containers. If not specified it will use docker.registry value in the nextflow.config file",
+)
+@click.option("-k", "--key", type=str, metavar="<test>", multiple=True, help="Run only these lint tests")
+@click.option("-a", "--all", is_flag=True, help="Run on all subworkflows")
+@click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures")
+@click.option("--local", is_flag=True, help="Run additional lint tests for local subworkflows")
+@click.option("--passed", is_flag=True, help="Show passed tests")
+@click.option(
+    "--sort-by",
+    type=click.Choice(["subworkflow", "test"]),
+    default="test",
+    help="Sort lint output by subworkflow or test name.",
+    show_default=True,
+)
+def lint(
+    ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by
+):  # pylint: disable=redefined-outer-name
+    """
+    Lint one or more subworkflows in a directory.
+
+    Checks DSL2 subworkflow code against nf-core guidelines to ensure
+    that all subworkflows follow the same standards.
+
+    Test subworkflows within a pipeline or a clone of the
+    nf-core/modules repository.
+    """
+    from nf_core.components.lint import LintException
+    from nf_core.subworkflows import SubworkflowLint
+
+    try:
+        subworkflow_lint = SubworkflowLint(
+            dir,
+            fail_warned=fail_warned,
+            registry=ctx.params["registry"],
+            remote_url=ctx.obj["modules_repo_url"],
+            branch=ctx.obj["modules_repo_branch"],
+            no_pull=ctx.obj["modules_repo_no_pull"],
+            hide_progress=ctx.obj["hide_progress"],
+        )
+        subworkflow_lint.lint(
+            subworkflow=subworkflow,
+            registry=registry,
+            key=key,
+            all_subworkflows=all,
+            print_results=True,
+            local=local,
+            show_passed=passed,
+            sort_by=sort_by,
+        )
+        if len(subworkflow_lint.failed) > 0:
+            sys.exit(1)
+    except LintException as e:
+        log.error(e)
+        sys.exit(1)
+    except (UserWarning, LookupError) as e:
+        log.critical(e)
+        sys.exit(1)
+
+
 # nf-core subworkflows info
 @subworkflows.command()
 @click.pass_context

nf_core/components/components_utils.py

@@ -128,7 +128,7 @@ def prompt_component_version_sha(component_name, component_type, modules_repo, i
 
 def get_components_to_install(subworkflow_dir):
     """
-    Parse the subworkflow test main.nf file to retrieve all imported modules and subworkflows.
+    Parse the subworkflow main.nf file to retrieve all imported modules and subworkflows.
     """
     modules = []
     subworkflows = []