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Merged
merged 3 commits into from
Feb 1, 2024
Merged

Update modules #506

merged 3 commits into from
Feb 1, 2024

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@ramprasadn
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@ramprasadn ramprasadn commented Feb 1, 2024

PR checklist

This PR updates the following modules

  1. genmod
  2. picard/markdup
  3. fastqc
  4. qualimap/bamqc
  5. samtools/stats
  • 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>).
  • 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).

@ramprasadn ramprasadn marked this pull request as ready for review February 1, 2024 12:45
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github-actions bot commented Feb 1, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3251b57

+| ✅ 178 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-01 12:47:03

@ramprasadn ramprasadn merged commit 32c518d into nf-core:dev Feb 1, 2024
@ramprasadn ramprasadn deleted the modules_update branch February 2, 2024 16:56
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@jemten jemten jemten approved these changes

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@ramprasadn @jemten