Merge pull request #1871 from nf-core/dev

Dev > Master for v2.6 release

Author: ewels

.github/workflows/rich-codex.yml

@@ -24,8 +24,7 @@ jobs:
         uses: ewels/rich-codex@v1
         env:
           COLUMNS: 100
-          NFCORE_LINT_HIDE_PROGRESS: true
-          NFCORE_MODULES_LINT_HIDE_PROGRESS: true
+          HIDE_PROGRESS: "true"
         with:
           commit_changes: "true"
           clean_img_paths: docs/images/*.svg

docs/api/_src/module_lint_tests/module_changes.md

@@ -0,0 +1,5 @@
+# module_changes
+
+```{eval-rst}
+.. automethod:: nf_core.modules.lint.ModuleLint.module_changes
+```

docs/api/_src/module_lint_tests/module_patch.md

@@ -0,0 +1,5 @@
+# module_patch
+
+```{eval-rst}
+.. automethod:: nf_core.modules.lint.ModuleLint.module_patch
+```

docs/api/_src/module_lint_tests/module_tests.md

@@ -0,0 +1,5 @@
+# module_tests
+
+```{eval-rst}
+.. automethod:: nf_core.modules.lint.ModuleLint.module_tests
+```

docs/api/_src/module_lint_tests/module_version.md

@@ -0,0 +1,5 @@
+# module_version
+
+```{eval-rst}
+.. automethod:: nf_core.modules.lint.ModuleLint.module_version
+```

docs/api/_src/pipeline_lint_tests/modules_structure.md

@@ -0,0 +1,5 @@
+# modules_structure
+
+```{eval-rst}
+.. automethod:: nf_core.lint.PipelineLint.modules_structure
+```

nf_core/lint/__init__.py

@@ -8,7 +8,7 @@
 import datetime
 import json
 import logging
-import re
+import os
 
 import git
 import rich
@@ -172,6 +172,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     from .files_unchanged import files_unchanged
     from .merge_markers import merge_markers
     from .modules_json import modules_json
+    from .modules_structure import modules_structure
     from .multiqc_config import multiqc_config
     from .nextflow_config import nextflow_config
     from .pipeline_name_conventions import pipeline_name_conventions
@@ -227,6 +228,7 @@ def _get_all_lint_tests(release_mode):
             "merge_markers",
             "modules_json",
             "multiqc_config",
+            "modules_structure",
         ] + (["version_consistency"] if release_mode else [])
 
     def _load(self):
@@ -311,7 +313,7 @@ def _lint_pipeline(self):
             rich.progress.BarColumn(bar_width=None),
             "[magenta]{task.completed} of {task.total}[reset] » [bold yellow]{task.fields[test_name]}",
             transient=True,
-            disable=self.hide_progress,
+            disable=self.hide_progress or os.environ.get("HIDE_PROGRESS", None) is not None,
         )
         with self.progress_bar:
             lint_progress = self.progress_bar.add_task(

nf_core/lint/modules_structure.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python
+
+import logging
+import os
+from pathlib import Path
+
+log = logging.getLogger(__name__)
+
+
+def modules_structure(self):
+    """
+    Check that the structure of the modules directory in a pipeline is the correct one:
+        modules/nf-core/TOOL/SUBTOOL
+
+    Prior to nf-core/tools release 2.6 the directory structure had an additional level of nesting:
+        modules/nf-core/modules/TOOL/SUBTOOL
+    """
+    wrong_location_modules = []
+    for directory, _, files in os.walk(Path(self.wf_path, "modules")):
+        if "main.nf" in files:
+            module_path = Path(directory).relative_to(Path(self.wf_path, "modules"))
+            parts = module_path.parts
+            # Check that there are modules installed directly under the 'modules' directory
+            if parts[1] == "modules":
+                wrong_location_modules.append(module_path)
+    # If there are modules installed in the wrong location
+    failed = []
+    passed = []
+    if len(wrong_location_modules) > 0:
+        failed = ["modules directory structure is outdated. Should be 'modules/nf-core/TOOL/SUBTOOL'"]
+    else:
+        passed = ["modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'"]
+    return {"passed": passed, "warned": [], "failed": failed, "ignored": []}

nf_core/modules/bump_versions.py

@@ -7,8 +7,8 @@
 from __future__ import print_function
 
 import logging
+import os
 import re
-from pathlib import Path
 
 import questionary
 import rich
@@ -55,6 +55,9 @@ def bump_versions(self, module=None, all_modules=False, show_uptodate=False):
         self.ignored = []
         self.show_up_to_date = show_uptodate
 
+        # Check modules directory structure
+        self.check_modules_structure()
+
         # Verify that this is not a pipeline
         self.dir, repo_type = nf_core.modules.module_utils.get_repo_type(self.dir)
         if not repo_type == "modules":
@@ -101,6 +104,7 @@ def bump_versions(self, module=None, all_modules=False, show_uptodate=False):
             rich.progress.BarColumn(bar_width=None),
             "[magenta]{task.completed} of {task.total}[reset] » [bold yellow]{task.fields[test_name]}",
             transient=True,
+            disable=os.environ.get("HIDE_PROGRESS", None) is not None,
         )
         with progress_bar:
             bump_progress = progress_bar.add_task(

nf_core/modules/create.py

@@ -88,6 +88,9 @@ def create(self):
         and matching Docker / Singularity images from BioContainers.
         """
 
+        # Check modules directory structure
+        self.check_modules_structure()
+
         # Check whether the given directory is a nf-core pipeline or a clone of nf-core/modules
         try:
             self.directory, self.repo_type = nf_core.modules.module_utils.get_repo_type(self.directory, self.repo_type)