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Fix --blacklist error and make fasta always available for IGV #291

Merged
merged 3 commits into from
Jun 9, 2023
Merged

Fix --blacklist error and make fasta always available for IGV #291

merged 3 commits into from
Jun 9, 2023

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JoseEspinosa
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Fix error when bed file is provided using the --blacklist parameter, fixes #268
Make genome fasta file always available when IGV process is run (not depending of --save_reference), closes #278

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 Jun 9, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8f0d882

+| ✅ 158 tests passed       |+
!| ❗   4 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
  • system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 23]
  • system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 36]
  • system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 41]

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-09 14:29:15

bjlang
bjlang approved these changes Jun 9, 2023
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LGTM

@bjlang bjlang merged commit a36bab8 into nf-core:dev Jun 9, 2023
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@bjlang bjlang bjlang approved these changes

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@JoseEspinosa @bjlang