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Add consistent support of .csi indices as alternative to .bai #328

Merged
merged 5 commits into from
Aug 11, 2023
Merged

Add consistent support of .csi indices as alternative to .bai #328

merged 5 commits into from
Aug 11, 2023

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bjlang
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@bjlang bjlang commented Aug 10, 2023 •
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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/atacseq 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>).
  • 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).

@bjlang bjlang requested a review from JoseEspinosa August 10, 2023 16:20
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github-actions bot commented Aug 10, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 79284fb

+| ✅ 156 tests passed       |+
!| ❗   3 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
  • system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 22]
  • system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 35]

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-11 18:02:55

@bjlang bjlang requested a review from drpatelh August 10, 2023 16:39
JoseEspinosa
JoseEspinosa requested changes Aug 11, 2023
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LGTM! Though I think I spotted a pair of typos

subworkflows/local/bam_filter_bamtools.nf Outdated Show resolved Hide resolved
workflows/atacseq.nf Outdated Show resolved Hide resolved
@bjlang bjlang linked an issue Aug 11, 2023 that may be closed by this pull request
CSI bam index not working #327
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@bjlang bjlang requested a review from JoseEspinosa August 11, 2023 14:06
JoseEspinosa
JoseEspinosa approved these changes Aug 11, 2023
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LGTM! Just a small suggestion about formatting

CHANGELOG.md Outdated Show resolved Hide resolved
@bjlang @JoseEspinosa
Update CHANGELOG.md
79284fb 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@bjlang bjlang merged commit 32513f8 into nf-core:dev Aug 11, 2023
@bjlang bjlang mentioned this pull request Aug 11, 2023
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@drpatelh drpatelh Awaiting requested review from drpatelh

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CSI bam index not working
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@bjlang @JoseEspinosa