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Improve file ignores in workflow file enumeration #3820

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3cae307
Improve file ignores in workflow file enumeration
jmuhlich Oct 8, 2025
5c6c50d
Update CHANGELOG.md
jmuhlich Oct 9, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -73,6 +73,7 @@
- Update GitHub Actions ([#3795](https://github.com/nf-core/tools/pull/3795))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.13.3 ([#3791](https://github.com/nf-core/tools/pull/3791))
- Update pre-commit hook pre-commit/pre-commit-hooks to v6 ([#3797](https://github.com/nf-core/tools/pull/3797))
- Improve file ignores in workflow file enumeration ([#3820](https://github.com/nf-core/tools/pull/3820))

## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08]

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14 changes: 10 additions & 4 deletions nf_core/utils.py
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Expand Up @@ -1648,15 +1648,21 @@ def get_wf_files(wf_path: Path):

wf_files = []

ignore = [".git/*"]
try:
with open(Path(wf_path, ".gitignore")) as f:
lines = f.read().splitlines()
ignore = [line for line in lines if line and not line.startswith("#")]
for line in f.read().splitlines():
if not line or line.startswith("#"):
continue
# Make trailing-slash patterns match their entire subtree
line = re.sub("/$", "/*", line)
ignore.append(line)
except FileNotFoundError:
ignore = []
pass

for path in Path(wf_path).rglob("*"):
if any(fnmatch.fnmatch(str(path), pattern) for pattern in ignore):
rpath = str(path.relative_to(wf_path))
if any(fnmatch.fnmatch(rpath, pattern) for pattern in ignore):
continue
if path.is_file():
wf_files.append(str(path))
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