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Fix trim multiqc #440

Merged
merged 18 commits into from
Nov 24, 2023
Merged

Fix trim multiqc #440

merged 18 commits into from
Nov 24, 2023

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rannick
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@rannick rannick commented Nov 22, 2023 •
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Update modules, and make sure multiqc displays the QC results properly

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/rnafusion 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>).
  • 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 Nov 22, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2cb7fc5

+| ✅ 158 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in WorkflowRnafusion.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-24 13:47:43

@rannick rannick marked this pull request as ready for review November 24, 2023 12:06
@rannick rannick self-assigned this Nov 24, 2023
fevac
fevac requested changes Nov 24, 2023
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don't forget to update the changelog. It would be nice to add the summary of all changes. To me this pr is a bit of a mix, for what I see:

  • changes multiqc report
  • updates versions for multiqc and samtools?
  • updates in trim workflow

assets/multiqc_config.yml Outdated Show resolved Hide resolved
assets/multiqc_config.yml Outdated Show resolved Hide resolved
conf/modules.config Show resolved Hide resolved
modules/nf-core/samtools/index/tests/csi.nextflow.config Show resolved Hide resolved
rannick and others added 3 commits November 24, 2023 14:02
@rannick @fevac
Update assets/multiqc_config.yml
04d57f0 
Co-authored-by: Eva C <29628428+fevac@users.noreply.github.com>
@rannick @fevac
Update assets/multiqc_config.yml
3fd0289 
Co-authored-by: Eva C <29628428+fevac@users.noreply.github.com>
@rannick
udpate changelog
113dd9e
@rannick rannick requested a review from fevac November 24, 2023 13:41
fevac
fevac approved these changes Nov 24, 2023
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🚀

@rannick rannick merged commit ba679fb into dev Nov 24, 2023
8 checks passed
@rannick rannick deleted the fix_trim_multiqc branch November 24, 2023 14:08
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@fevac fevac fevac approved these changes

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