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add realigned bam export possibilities to gatk4_haplotypecaller #864

Merged
merged 9 commits into from
Nov 24, 2022
Merged

add realigned bam export possibilities to gatk4_haplotypecaller #864

merged 9 commits into from
Nov 24, 2022

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maxulysse
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@maxulysse maxulysse commented Nov 24, 2022 •
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  • update gatk4/haplotypecaller
  • gather realigned bams

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).

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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 @maxulysse,

It looks like this pull-request is has been made against the maxulysse/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 maxulysse/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
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@nf-core-bot fix linting pretty please

@maxulysse maxulysse changed the base branch from master to dev November 24, 2022 11:01
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github-actions bot commented Nov 24, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5c6017a

+| ✅ 151 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_description - No description provided in schema for parameter: cnvkit_reference

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-24 13:50:46

@maxulysse
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@nf-core-bot fix linting pretty please once more time

@FriederikeHanssen
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Changelog?

@maxulysse maxulysse merged commit 36bb01d into nf-core:dev Nov 24, 2022
@maxulysse maxulysse deleted the dev_ultima branch November 24, 2022 15:40
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen @nf-core-bot