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Remove merge_haplotypecaller_filtered #605

Merged
merged 20 commits into from
Jun 30, 2022
Merged

Remove merge_haplotypecaller_filtered #605

merged 20 commits into from
Jun 30, 2022

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WackerO
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@WackerO WackerO commented Jun 24, 2022 •
edited by FriederikeHanssen
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Edited by @FriederikeHanssen : This PR changes the behavior of the Haplotypecaller single sample mode to not parallelize via scatter/gather. The reason being that often FilterVariantTranches fails on smaller regions (even for WGS) if no SNP is present in this particular one. Instead all regions are run together to avoid this kind of behavior.

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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).
  • 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).

@WackerO WackerO requested a review from maxulysse as a code owner June 24, 2022 09:30
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github-actions bot commented Jun 24, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d59906e

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ 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 2.4.1
  • Run at 2022-06-30 12:27:27

@FriederikeHanssen FriederikeHanssen requested review from maxulysse and removed request for maxulysse June 29, 2022 08:35
maxulysse
maxulysse approved these changes Jun 30, 2022
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LGTM

@FriederikeHanssen FriederikeHanssen merged commit 135ec96 into nf-core:dev Jun 30, 2022
@WackerO WackerO deleted the single branch July 27, 2022 09:01
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen requested changes

@maxulysse maxulysse maxulysse approved these changes

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@WackerO @maxulysse @FriederikeHanssen