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Optional alignment thumbnails in the MultiQC report.#111

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charles-plessy merged 3 commits into
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multiqc-thumbs-issue-93
May 26, 2026
Merged

Optional alignment thumbnails in the MultiQC report.#111
charles-plessy merged 3 commits into
devfrom
multiqc-thumbs-issue-93

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@charles-plessy charles-plessy commented May 25, 2026

Adds a new option --multiqc_thumbs that defines a pixel size for alignment thumbnails to be displayed in the MultiQC report. Defaults to zero for no plots.

Closes #93

PR checklist

  • 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/pairgenomealign 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>).
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  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
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Adds a new option `--multiqc_thumb` that defines a pixel size for
alignment thumbnails to be displayed in the MultiQC report.  Defaults
to zero for no plots.

Closes #93
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@piplus2 piplus2 left a comment

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LGTM!

@piplus2
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piplus2 commented May 25, 2026

the only thing I think worth checking is that base64 -w 0 works on MacOS too.

The option `-w` is not available on Macintosh.

Thanks @piplus2 for catching this issue.
@charles-plessy charles-plessy merged commit 715fd61 into dev May 26, 2026
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@charles-plessy charles-plessy deleted the multiqc-thumbs-issue-93 branch May 26, 2026 00:44
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2 participants