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Mindagap skip #78

Merged
merged 4 commits into from
Sep 24, 2024
Merged

Mindagap skip #78

merged 4 commits into from
Sep 24, 2024

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kbestak
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@kbestak kbestak commented Sep 10, 2024 •
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Added skip mindagap parameter - if no gaps in input images, mindagap isn't necessary and adapted the workflow.
Adapted collect_QC.py to take into account the raw input file.
Addresses: #74

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/molkart branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core 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).

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github-actions bot commented Sep 10, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6dbf1b1

+| ✅ 211 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-10 15:22:14

@FloWuenne FloWuenne self-requested a review September 24, 2024 14:33
FloWuenne
FloWuenne approved these changes Sep 24, 2024
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LGTM ⭐ 🚀 . Tests pass on gitpod and AWS with and without setting the new flag!

I got caught up for a second because the MultiQC report doesn't include the fix you recently introduced, but I saw this branch was just created before the merge into dev.

@kbestak kbestak merged commit b12929c into nf-core:dev Sep 24, 2024
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@FloWuenne FloWuenne FloWuenne approved these changes

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@kbestak @FloWuenne