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Ngscheckmate fix #1381

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Merged
merged 2 commits into from
Jan 25, 2024
Merged

Ngscheckmate fix #1381

merged 2 commits into from
Jan 25, 2024

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SPPearce
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Swapped the NGSCheckMate bed file for GRCh37.GATK to the one without "chr" prefix.

@SPPearce SPPearce changed the base branch from master to dev January 24, 2024 18:00
@nf-core nf-core deleted a comment from github-actions bot Jan 24, 2024
FriederikeHanssen
FriederikeHanssen approved these changes Jan 24, 2024
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@FriederikeHanssen FriederikeHanssen left a comment

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any upload to igenomes needed?

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github-actions bot commented Jan 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 42d3fd0

+| ✅ 147 tests passed       |+
#| ❔  10 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
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • 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 2.11.1
  • Run at 2024-01-24 18:02:02

@SPPearce
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any upload to igenomes needed?

No, the file is already there and being used in Ensembl.GRCh37

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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @SPPearce,

It looks like this pull-request is has been made against the nf-core/sarek master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/sarek dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@maxulysse maxulysse merged commit 0b5afa8 into dev Jan 25, 2024
@maxulysse maxulysse deleted the ngscheckmate_fix branch February 15, 2024 17:27
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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

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3 participants

@SPPearce @FriederikeHanssen @maxulysse