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Switch from macs2 to macs3 #404

Merged
merged 8 commits into from
Jul 23, 2024
Merged

Switch from macs2 to macs3 #404

merged 8 commits into from
Jul 23, 2024

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JoseEspinosa
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Closes #378

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>).
  • 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).

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github-actions bot commented Jul 23, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7238956

+| ✅ 223 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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!

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-23 11:00:23

mirpedrol
mirpedrol approved these changes Jul 23, 2024
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LGTM! only two small comments :)

conf/modules.config
@@ -579,7 +579,7 @@ if (!params.skip_peak_annotation) {
ext.args = '-gid'
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The name in the previous line is not updated BAM_PEAKS_CALL_QC_ANNOTATE_MACS2_HOMER:HOMER_ANNOTATEPEAKS

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@JoseEspinosa JoseEspinosa Jul 23, 2024 •
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Good spot, did not saved the change 😓

test.csv Outdated
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This was probably added by mistake? 🙂

@JoseEspinosa JoseEspinosa merged commit 9fe5767 into nf-core:dev Jul 23, 2024
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@JoseEspinosa JoseEspinosa mentioned this pull request Jul 23, 2024
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@mirpedrol mirpedrol mirpedrol approved these changes

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@JoseEspinosa @mirpedrol