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Some fixes #339

Merged
merged 24 commits into from
Apr 18, 2023
Merged

Some fixes #339

merged 24 commits into from
Apr 18, 2023

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JoseEspinosa
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@JoseEspinosa JoseEspinosa commented Apr 17, 2023 •
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Add back skip_spp parameter (fixes #311)
Install all available subworkflows in nf-core and refactor the code accordingly
Update bowtie2/align to fix the download of the container by tools (fixes #318)

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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github-actions bot commented Apr 17, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit aece0fb

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-04-18 20:49:47

@JoseEspinosa JoseEspinosa marked this pull request as ready for review April 18, 2023 15:24
@JoseEspinosa JoseEspinosa mentioned this pull request Apr 18, 2023
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bjlang
bjlang reviewed Apr 18, 2023
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workflows/chipseq.nf Outdated
Comment on lines 312 to 317
BAM_FILTER_BAMTOOLS
.out
.bam
.map {
[ it[0], it[1], [] ]
}
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What is this for?

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A view that I forgot to remove, thanks for spotting it!

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Fix in 6a75945

bjlang
bjlang approved these changes Apr 18, 2023
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LGTM 🚀

@JoseEspinosa JoseEspinosa merged commit 3b94a84 into nf-core:dev Apr 18, 2023
This was referenced Jul 24, 2024
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@bjlang bjlang bjlang approved these changes

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@JoseEspinosa @bjlang