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Strict mode #242

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@fasterius fasterius commented Jan 20, 2026 •
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This PR contains (non-exhaustive) changes related to both the new Nextflow strict syntax, as well as some harmonisation and increased readability across the pipeline code.

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

@fasterius
Replace Channel with channel
e151e12
@fasterius
Move embedded param references to root workflow
4494f12
@fasterius
Separate long lines for increased code readability
eb49fdb 
Separate long lines containing e.g. extensive maps and process calls
with many inputs to increase code readability. Additionally, some minor
formatting and harmonisation throughout.
@fasterius
Remove unused config reference
04dafa3
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nf-core-bot commented Jan 20, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@fasterius fasterius requested a review from nictru January 20, 2026 09:45
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nictru commented Jan 20, 2026

Amazing thanks! I have been thinking about doing something like this! Will look at it soon

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fasterius commented Jan 20, 2026

No worries! I asked for a review a little prematurely, gotta fix some issues first, so no rush.

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fasterius commented Jan 22, 2026

I think I'm going to need some help with these conflicts, @nictru. You've removed some tests and there's the new condition_col meta variable, and I'm not entirely sure how it fits into my refactoring for the strict mode. If you like we can have a Zoom and do it together.

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@nictru nictru Awaiting requested review from nictru

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