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Change unnecessary MultiQC containers to nf-core/ubuntu:20.04 #651

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merged 2 commits into from
Aug 21, 2024
Merged

Change unnecessary MultiQC containers to nf-core/ubuntu:20.04 #651

merged 2 commits into from
Aug 21, 2024

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harper357
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Re: slack question about old MultiQC containers

A small PR to replace unnecessary MultiQC containers with nf-core/ubuntu:20.04.

PR checklist

  • This comment contains a description of changes (with reason).
  • 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>).
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

jfy133
jfy133 approved these changes Aug 20, 2024
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LGTM! Thank you @harper357 !

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github-actions bot commented Aug 20, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit bd0ef3b

+| ✅ 307 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-20 06:38:14

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jfy133 commented Aug 20, 2024

@harper357 do you plan to also do the custom/dumpsoftwareversions one to on nf-core/modules? If yes we could wait for that and include it in this PR, if not I can do it and do it in a separate one :)

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It looks like dumpsoftwareversions is out of date too. I think I have time to make a PR over there today/tomorrow, so I am fine having this one wait until that one gets merged if you are

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nf-core/modules#6224

@harper357
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I was testing the latest version of nf-core/modules/multiqc, but it crashes because it has two new optional inputs.

I could update workflows/mag.nf and nextflow.config to support it, but then it seems like a larger PR than you might want. Do you want that here or in a new PR?

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jfy133 commented Aug 21, 2024

OK nice :D We will merge this is in now, I have a wider question for the community about the MultiQC container in teh dumpsoftwareversions module, so I'll raise that on slack first

@jfy133 jfy133 merged commit 6a40905 into nf-core:dev Aug 21, 2024
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@jfy133 jfy133 mentioned this pull request Aug 22, 2024
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