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Updating samtools #1408

Merged
merged 17 commits into from
Feb 16, 2024
Merged

Updating samtools #1408

merged 17 commits into from
Feb 16, 2024

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asp8200
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@asp8200 asp8200 commented Feb 15, 2024 •
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In this PR, we just update the "pure" samtools-modules. The modules using mulled containers with samtools will be updated in a later PR.

maxulysse
maxulysse reviewed Feb 15, 2024
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Looking good already.
Don't forget to update CHANGELOG

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github-actions bot commented Feb 15, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6ef5dbd

+| ✅ 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 2024-02-16 12:42:36

@maxulysse maxulysse mentioned this pull request Feb 15, 2024
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ok, good news, we fixed the samtools/view tests

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asp8200 commented Feb 15, 2024

Is it a similar problem with samtools/mpileup?

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Is it a similar problem with samtools/mpileup?

Unfortunately no

@maxulysse maxulysse marked this pull request as ready for review February 16, 2024 12:33
maxulysse
maxulysse reviewed Feb 16, 2024
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CHANGELOG.md Outdated Show resolved Hide resolved
asp8200 and others added 2 commits February 16, 2024 13:35
@asp8200 @maxulysse
Update CHANGELOG.md
6c1634a 
Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se>
@asp8200
Adding samtools-update to Dependencies table
6ef5dbd
@maxulysse maxulysse merged commit e92cfb3 into nf-core:dev Feb 16, 2024
51 of 53 checks passed
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