diff --git a/README.md b/README.md index 88542d2176..cd7ca1f8dc 100644 --- a/README.md +++ b/README.md @@ -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). + diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py index 00031d8b62..ce26306881 100644 --- a/nf_core/modules/lint/module_tests.py +++ b/nf_core/modules/lint/module_tests.py @@ -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())