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add fastp and ngsbits to multiqc input#647

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ramprasadn merged 13 commits into
nf-core:devfrom
genomic-medicine-sweden:add-fastp-to-multiqc
Nov 15, 2024
Merged

add fastp and ngsbits to multiqc input#647
ramprasadn merged 13 commits into
nf-core:devfrom
genomic-medicine-sweden:add-fastp-to-multiqc

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@peterpru

@peterpru peterpru commented Nov 11, 2024 •
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Add fastp and ngsbits output files to the input of multiqc.

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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

@github-actions

github-actions Bot commented Nov 11, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b8deb72

+| ✅ 201 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-15 14:09:45

@peterpru peterpru changed the title add file to multiqc input add fastp and ngsbits to multiqc input Nov 11, 2024
@peterpru peterpru self-assigned this Nov 11, 2024
@peterpru peterpru marked this pull request as ready for review November 15, 2024 13:44
@ramprasadn ramprasadn merged commit fa781f6 into nf-core:dev Nov 15, 2024
@ramprasadn ramprasadn deleted the add-fastp-to-multiqc branch March 30, 2026 21:07
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@ramprasadn ramprasadn ramprasadn approved these changes

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