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switch to using --write-index instead of samtools index #1338

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switch to using --write-index instead of samtools index #1338

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FriederikeHanssen
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@FriederikeHanssen FriederikeHanssen commented Nov 23, 2023 •
edited

Closes #1121

well aware that modules here are changed locally. Want to test all works before going to update them in nf-core/modules.

What to update upstream:

  • CNVKit batch
  • GATK4 Markduplicates
  • Samtools convert
  • Samtools merge

@FriederikeHanssen FriederikeHanssen marked this pull request as draft November 23, 2023 13:22
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github-actions bot commented Nov 23, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b75a8f7

+| ✅ 144 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-23 14:05:19

@FriederikeHanssen
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Benchmarked this quickly using the Co2 footprint, which is now higher. I will dig more into it to see if this is due to some general fluctuation on the cluster and how other metrics look like.

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Don't see any particular decreases in mem or cpu or work storage. So benefit is avoiding spinning up more machines/reducing number of jobs submitted.

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