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don't use freebayes for bcftools sort on joint germline #741

Merged
merged 5 commits into from
Sep 8, 2022
Merged

don't use freebayes for bcftools sort on joint germline #741

merged 5 commits into from
Sep 8, 2022

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FriederikeHanssen
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@FriederikeHanssen FriederikeHanssen commented Sep 8, 2022 •
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Close #737

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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github-actions bot commented Sep 8, 2022 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit bcfb73e

+| ✅ 151 tests passed       |+
#| ❔   4 tests were ignored |#

❔ Tests ignored:

  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.5.1
  • Run at 2022-09-08 13:46:10

@FriederikeHanssen
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don't merge just yet, I am investigating something weird in the naming, can't convert it back to draft

maxulysse
maxulysse approved these changes Sep 8, 2022
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LGTM

@maxulysse maxulysse marked this pull request as draft September 8, 2022 12:39
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Back to draft it is

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review September 8, 2022 13:33
@FriederikeHanssen FriederikeHanssen merged commit 6fc7d5f into nf-core:dev Sep 8, 2022
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@maxulysse maxulysse maxulysse approved these changes

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@FriederikeHanssen @maxulysse