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Update modules #217

Merged
merged 23 commits into from
Aug 1, 2024
Merged

Update modules #217

merged 23 commits into from
Aug 1, 2024

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atrigila
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@atrigila atrigila commented Jul 31, 2024 •
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nf-core template is up-to-date.
Modules and tests are updated in this PR.
#198

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).

@atrigila atrigila self-assigned this Jul 31, 2024
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @atrigila,

It looks like this pull-request is has been made against the atrigila/demultiplex master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the atrigila/demultiplex dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@atrigila atrigila changed the base branch from master to dev July 31, 2024 20:10
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github-actions bot commented Jul 31, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0070b64

+| ✅ 187 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ 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 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
  • schema_description - Ungrouped param in schema: checkqc_config

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-01 17:05:40

@atrigila
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atrigila commented Aug 1, 2024

The new update from multiqc changes the way files are named (e.g. from multiqc_bcl2fastq_bylane.txt to bcl2fastq_lane_counts.txt). Therefore, the previous snapshots of bcl2fastq and bclconvert are failing. However, the multiqc report still generates those sections (e.g. clusters by lane or clusters by sample, or fastp module). For that reason, I am changing the filenames of the snapshots.

@atrigila atrigila marked this pull request as ready for review August 1, 2024 16:18
@atrigila atrigila requested review from blajoie and a team as code owners August 1, 2024 16:18
@atrigila atrigila requested review from glichtenstein and removed request for a team August 1, 2024 16:18
@apeltzer apeltzer added this to the 1.5.0 milestone Aug 1, 2024
@apeltzer apeltzer merged commit 7697ba1 into nf-core:dev Aug 1, 2024
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@apeltzer apeltzer mentioned this pull request Aug 12, 2024
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@apeltzer apeltzer apeltzer approved these changes

@blajoie blajoie Awaiting requested review from blajoie blajoie is a code owner

@glichtenstein glichtenstein Awaiting requested review from glichtenstein glichtenstein is a code owner automatically assigned from nf-core/demultiplex

@nschcolnicov nschcolnicov Awaiting requested review from nschcolnicov

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