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Update Modules

Open apeltzer opened this issue 1 year ago • 2 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).

apeltzer avatar Sep 17 '24 14:09 apeltzer

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

Posted for pipeline commit b40ecc6

+| ✅ 190 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.5.1
  • 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 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 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 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 2024-10-03 12:21:33

github-actions[bot] avatar Sep 17 '24 14:09 github-actions[bot]

Seems like after the new MultiQC version, it no longer raises an error but the MultiQC report is still not displaying the Kraken section. The old issue explaining this is https://github.com/MultiQC/MultiQC/issues/2801 and was closed after releasing version 1.25.

I created a new issue to follow up on the missing kraken report: https://github.com/MultiQC/MultiQC/issues/2876

MultiQC report not displaying kraken: image

nschcolnicov avatar Sep 24 '24 17:09 nschcolnicov

I had to update some of the snaps, because the md5sums of some of the multiqc plots changed, due to them now displaying the numerical values with one decimal place: image

nschcolnicov avatar Oct 02 '24 21:10 nschcolnicov