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Strict syntax and modules update#273

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LouisLeNezet wants to merge 17 commits intonf-core:devfrom
LouisLeNezet:strict_syntax
Open

Strict syntax and modules update#273
LouisLeNezet wants to merge 17 commits intonf-core:devfrom
LouisLeNezet:strict_syntax

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@LouisLeNezet LouisLeNezet commented Mar 17, 2026

PR checklist

Due to the multiqc update, the file name of glimpse_concordance in the multiqc report have changed.
The md5sum are all the same except for glimpse-err-spl-table.txt due to a column header change.

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/phaseimpute branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@LouisLeNezet LouisLeNezet changed the title Strict syntax Strict syntax and modules update Mar 17, 2026
@LouisLeNezet LouisLeNezet requested a review from atrigila March 19, 2026 15:50
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