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Add ataqv_mito_reference parameter #294

Merged
merged 3 commits into from
Jun 29, 2023
Merged

Add ataqv_mito_reference parameter #294

merged 3 commits into from
Jun 29, 2023

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JoseEspinosa
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Add ataqv_mito_reference parameter. This parameter enables a different mitochondrial tag to ATAQV since as explained in #262 when dealing with plant and similar organisms sometimes more than one chromosome has to be filtered out. In these cases, the chromosomes can be filtered out setting mito_name this way: --mito_name='mito_id1|mito_id2' . However, this broke ataqv since its mitochondrial-reference-name parameter directly took the mito_name value. This can be solved now by providing a different tag using the ataqv_mito_reference. When not set, the behavior will be as it was until now, and ataqv_mito_reference will be set by default to the same value as mito_name.
Closes #262

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 28, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3bbbf4d

+| ✅ 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 2023-06-29 17:28:47

@JoseEspinosa JoseEspinosa marked this pull request as ready for review June 29, 2023 08:16
bjlang
bjlang approved these changes Jun 29, 2023
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LGTM!

@JoseEspinosa JoseEspinosa merged commit 6462faf into nf-core:dev Jun 29, 2023
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@bjlang bjlang bjlang approved these changes

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@JoseEspinosa @bjlang