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Add kraken step aratz

Open nschcolnicov opened this issue 1 year ago • 3 comments

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/demultiplex 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).

nschcolnicov avatar Aug 01 '24 17:08 nschcolnicov

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 1293d6f

+| ✅ 190 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

:grey_question: Tests ignored:

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-07 15:08:40

github-actions[bot] avatar Aug 01 '24 17:08 github-actions[bot]

@apeltzer @atrigila Ready for review!

nschcolnicov avatar Aug 02 '24 20:08 nschcolnicov

@grst I addressed the comments, should I go ahead and merge it?

nschcolnicov avatar Aug 06 '24 16:08 nschcolnicov

I think it's fine now 👍

apeltzer avatar Aug 06 '24 21:08 apeltzer