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Improve MultiQC report #308

Merged
merged 8 commits into from
Jan 26, 2024
Merged

Improve MultiQC report #308

merged 8 commits into from
Jan 26, 2024

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grst
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@grst grst commented Jan 26, 2024 •
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Merge #307 first!

  • Add FASTQC on deduplicated reads
  • make sure the different FASTQC report actually show up in the multiqc report
  • check other multiqc modules if they should show up separately (e.g. samtools stats)
  • reorder multiqc report such that it makes sense (and add descriptions where necessary)
  • Update CHANGELOG

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/smrnaseq 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).

grst added 6 commits January 26, 2024 10:38
@grst
Remove redundant fastq option
4b2bf89
@grst
Clean up config
17f2ae5 
Replicating the if/else logic from the main workflow is
not necessary, since now, by default
nextflow.enable.configProcessNamesValidation = false
@grst
WIP reorganize config
306cd4e
@grst
More config updates
ede1ee9
@grst
Final outputpath fixes
e707e28
@grst
Include MultiQC report for deduplicated fastqs
a001dbf
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github-actions bot commented Jan 26, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8dbd139

+| ✅ 162 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.3.0
  • pipeline_todos - TODO string in WorkflowSmrnaseq.groovy: Optionally add in-text citation tools to this list.
  • schema_description - No description provided in schema for parameter: save_merged

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-26 14:53:52

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grst commented Jan 26, 2024 •
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@nf-core-bot fix linting

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grst commented Jan 26, 2024

@nf-core-bot fix linting

@apeltzer apeltzer marked this pull request as ready for review January 26, 2024 15:16
apeltzer
apeltzer approved these changes Jan 26, 2024
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Thanks - I think that helps quite a bit with debugging / checking the pipeline outputs :)

@apeltzer apeltzer merged commit 8121dec into dev Jan 26, 2024
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@apeltzer apeltzer deleted the more-fastqc branch January 26, 2024 15:16
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