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fix: relax stub .gz linting regex to accept echo without arguments #4323

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fix: relax stub .gz linting regex to accept echo without arguments #4323

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fix: relax stub .gz linting regex to accept echo without args
handsomesix Jun 11, 2026
c2109c6
trigger CI: re-run checks on dev branch
handsomesix Jun 12, 2026
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -80,3 +80,4 @@ If you use `nf-core tools` in your work, please cite the `nf-core` publication a
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).

4 changes: 2 additions & 2 deletions nf_core/modules/lint/module_tests.py
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Expand Up @@ -329,8 +329,8 @@ def _check_stub_gzip_syntax(module: NFCoreComponent):
if not line or line.startswith(("//", "#")):
continue

# The ONLY valid pattern is: echo "" | gzip > file.gz
valid_pattern = r'echo\s+""\s*\|\s*gzip\s*>\s*.*\.gz$'
# Valid patterns: echo "" | gzip >, echo '' | gzip >, or echo | gzip >
valid_pattern = r'''echo(?:\s+(?:""|''))?\s*\|\s*gzip\s*>\s*.*\.gz$'''

if not re.search(valid_pattern, line):
invalid_gz_patterns.append(line.strip())
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