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Update mulled-containers to samtools v1.19.2 #1412

Merged
merged 18 commits into from
Feb 20, 2024
Merged

Update mulled-containers to samtools v1.19.2 #1412

merged 18 commits into from
Feb 20, 2024

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asp8200
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@asp8200 asp8200 commented Feb 16, 2024 •
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Updating all mulled-containers with samtools so that they use v1.19.2 of samtools. (Also updating some cnvkit-modules which unnecessarily included samtools in environment.yml.)

I think I finally managed to update all occurrence of samtools to v1.19.2 - except gatk4/markduplicates - since that will be updated as part of the general update to GATK4.5.

image

NOTE: The nf-test bwamem2/mem has been disabled as it is failing - perhaps due to some conflicting configs.

The Sentieon tests are still disabled.

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github-actions bot commented Feb 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1bcdf57

+| ✅ 188 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • 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
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-20 14:48:28

@asp8200 asp8200 changed the title Update mulled-containers to samtools v.1.19.2 Update mulled-containers to samtools v1.19.2 Feb 19, 2024
@asp8200 asp8200 marked this pull request as ready for review February 19, 2024 11:32
@maxulysse maxulysse marked this pull request as draft February 19, 2024 11:44
maxulysse
maxulysse previously approved these changes Feb 19, 2024
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maxulysse
maxulysse previously approved these changes Feb 20, 2024
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@asp8200 asp8200 requested a review from maxulysse February 20, 2024 14:46
@asp8200 asp8200 marked this pull request as ready for review February 20, 2024 14:56
@maxulysse maxulysse merged commit fa75797 into nf-core:dev Feb 20, 2024
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@asp8200 asp8200 mentioned this pull request Feb 22, 2024
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@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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