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Updated docs of bcftools stats variant depth #788

Merged
merged 3 commits into from
Oct 11, 2022
Merged

Updated docs of bcftools stats variant depth #788

merged 3 commits into from
Oct 11, 2022

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SusiJo
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@SusiJo SusiJo commented Oct 11, 2022

This PR refers to issue #779: Strelka2 does not produce the necessary INFO/DP field which is required for bcftools stats to extract the variant depth distribution. So for variant callers that natively report this field, the depth distribution plot should not be empty independent of WGS/WES mode. There will also be a MultiQC container update soon to prevent showing an empty depth distribution plot in the MultiQC report.

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).

@SusiJo
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SusiJo commented Oct 11, 2022

Concerning the issue with Strelka2 I've opened an issue here

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github-actions bot commented Oct 11, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9eb0df6

+| ✅ 154 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 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

❔ 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 2.6
  • Run at 2022-10-11 09:35:33

FriederikeHanssen
FriederikeHanssen approved these changes Oct 11, 2022
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@FriederikeHanssen FriederikeHanssen merged commit 53a4245 into nf-core:dev Oct 11, 2022
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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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