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Sambamba #1368

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stavgrossfeld
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@github-actions GitHub Actions
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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 @stavgrossfeld,

It looks like this pull-request is has been made against the stavgrossfeld/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 stavgrossfeld/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!

@github-actions GitHub Actions
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github-actions bot commented Dec 29, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 35ba757

+| ✅ 146 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 2023-12-30 01:43:40

@stavgrossfeld stavgrossfeld changed the base branch from master to dev December 29, 2023 08:59
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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen will be requested when the pull request is marked ready for review FriederikeHanssen is a code owner

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse will be requested when the pull request is marked ready for review maxulysse is a code owner

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