Merge branch 'dev' into pytest-requirements

Author: fabianegli

.github/workflows/create-lint-wf.yml

@@ -80,9 +80,13 @@ jobs:
       - name: nf-core modules update
         run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview
 
+      # Remove TODO statements
+      - name: remove TODO
+        run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
+
       # Run nf-core linting
       - name: nf-core lint
-        run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored
+        run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored --fail-warned
 
       # Run the other nf-core commands
       - name: nf-core list
@@ -98,7 +102,7 @@ jobs:
         run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
 
       - name: nf-core lint in release mode
-        run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored --release
+        run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
 
       - name: nf-core modules install
         run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force

CHANGELOG.md

@@ -13,6 +13,8 @@
 ### General
 
 - Updated the package requirements to prevent defunct installations of nf-core [#1620](https://github.com/nf-core/tools/pull/1620)
+- Add `--fail-warned` flag to `nf-core lint` to make warnings fail [#1593](https://github.com/nf-core/tools/pull/1593)
+- Add `--fail-warned` flag to pipeline linting workflow [#1593](https://github.com/nf-core/tools/pull/1593)
 
 ### Modules
 

nf_core/__main__.py

@@ -301,9 +301,10 @@ def create(name, description, author, version, no_git, force, outdir):
 @click.option("-k", "--key", type=str, metavar="<test>", multiple=True, help="Run only these lint tests")
 @click.option("-p", "--show-passed", is_flag=True, help="Show passing tests on the command line")
 @click.option("-i", "--fail-ignored", is_flag=True, help="Convert ignored tests to failures")
+@click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures")
 @click.option("--markdown", type=str, metavar="<filename>", help="File to write linting results to (Markdown)")
 @click.option("--json", type=str, metavar="<filename>", help="File to write linting results to (JSON)")
-def lint(dir, release, fix, key, show_passed, fail_ignored, markdown, json):
+def lint(dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json):
     """
     Check pipeline code against nf-core guidelines.
 
@@ -325,7 +326,7 @@ def lint(dir, release, fix, key, show_passed, fail_ignored, markdown, json):
     # Run the lint tests!
     try:
         lint_obj, module_lint_obj = nf_core.lint.run_linting(
-            dir, release, fix, key, show_passed, fail_ignored, markdown, json
+            dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json
         )
         if len(lint_obj.failed) + len(module_lint_obj.failed) > 0:
             sys.exit(1)

nf_core/lint/__init__.py

@@ -29,7 +29,15 @@
 
 
 def run_linting(
-    pipeline_dir, release_mode=False, fix=(), key=(), show_passed=False, fail_ignored=False, md_fn=None, json_fn=None
+    pipeline_dir,
+    release_mode=False,
+    fix=(),
+    key=(),
+    show_passed=False,
+    fail_ignored=False,
+    fail_warned=False,
+    md_fn=None,
+    json_fn=None,
 ):
     """Runs all nf-core linting checks on a given Nextflow pipeline project
     in either `release` mode or `normal` mode (default). Returns an object
@@ -62,7 +70,7 @@ def run_linting(
     # Create the lint object
     pipeline_keys = list(set(key).intersection(set(PipelineLint._get_all_lint_tests(release_mode)))) if key else []
 
-    lint_obj = PipelineLint(pipeline_dir, release_mode, fix, pipeline_keys, fail_ignored)
+    lint_obj = PipelineLint(pipeline_dir, release_mode, fix, pipeline_keys, fail_ignored, fail_warned)
 
     # Load the various pipeline configs
     lint_obj._load_lint_config()
@@ -167,7 +175,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     from .template_strings import template_strings
     from .version_consistency import version_consistency
 
-    def __init__(self, wf_path, release_mode=False, fix=(), key=(), fail_ignored=False):
+    def __init__(self, wf_path, release_mode=False, fix=(), key=(), fail_ignored=False, fail_warned=False):
         """Initialise linting object"""
 
         # Initialise the parent object
@@ -179,6 +187,7 @@ def __init__(self, wf_path, release_mode=False, fix=(), key=(), fail_ignored=Fal
         self.lint_config = {}
         self.release_mode = release_mode
         self.fail_ignored = fail_ignored
+        self.fail_warned = fail_warned
         self.failed = []
         self.ignored = []
         self.fixed = []
@@ -314,7 +323,10 @@ def _lint_pipeline(self):
                 for test in test_results.get("fixed", []):
                     self.fixed.append((test_name, test))
                 for test in test_results.get("warned", []):
-                    self.warned.append((test_name, test))
+                    if self.fail_warned:
+                        self.failed.append((test_name, test))
+                    else:
+                        self.warned.append((test_name, test))
                 for test in test_results.get("failed", []):
                     self.failed.append((test_name, test))
                 if test_results.get("could_fix", False):