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

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handsomesix wants to merge 2 commits into
nf-core:devfrom
handsomesix:fix/stub-gzip-linting
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fix: relax stub .gz linting regex to accept echo without arguments#4323
handsomesix wants to merge 2 commits into
nf-core:devfrom
handsomesix:fix/stub-gzip-linting

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@handsomesix

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Summary

Fixes #4231 by relaxing the stub .gz linting regex to make the echo argument optional.

Changes

  • Updated the stub .gz linting regex to accept echo, echo '', and echo "" as valid arguments before piping to gzip.
  • Previously only echo "" was accepted; echo | gzip > now also passes lint.

Tests

Verified that existing valid patterns continue to pass and that invalid syntax (touch, non-empty echo strings) is still correctly flagged.

Risk

Low. The change only broadens an existing regex match — it does not affect any other lint rule or module behavior.

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This PR is against the main branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @handsomesix,

It looks like this pull-request is has been made against the handsomesix/tools main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the handsomesix/tools dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@handsomesix handsomesix force-pushed the fix/stub-gzip-linting branch from 1fbb006 to 6391130 Compare June 12, 2026 11:57
@handsomesix handsomesix changed the base branch from main to dev June 12, 2026 12:31
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stub .gz linting is too restrictive

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