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Add variant caller to bcftools/vcftools + multiqc #618

Merged
merged 17 commits into from
Jul 14, 2022
Merged

Add variant caller to bcftools/vcftools + multiqc #618

merged 17 commits into from
Jul 14, 2022

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SusiJo
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@SusiJo SusiJo commented Jul 5, 2022 •
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Also close #621

PR checklist

This PR fixes the sample names of the files in results/reports/bcftools, results/reports/vcftools and results/multiqc and adds the variant caller to the sample name.

  • 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).

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github-actions bot commented Jul 5, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 43a0a52

+| ✅ 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 2022-07-14 08:26:38

@maxulysse
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Is this PR closing this one too: #526

@maxulysse maxulysse mentioned this pull request Jul 13, 2022
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@SusiJo
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SusiJo commented Jul 13, 2022

Still need to remove uncommented stuff and some dump statements. But most of it can be reviewed already.
Especially the prefixes in the modules.config should be reviewed cautiously. Hope I'm not introducing any new bugs that the tests do not cover.

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SusiJo commented Jul 13, 2022

This should also fix the null folder of tiddit and issues related to targets.bed.

@SusiJo SusiJo marked this pull request as ready for review July 13, 2022 14:39
@SusiJo SusiJo requested a review from maxulysse as a code owner July 13, 2022 14:39
@SusiJo SusiJo requested a review from FriederikeHanssen July 13, 2022 14:40
maxulysse
maxulysse reviewed Jul 13, 2022
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Just minor comments.
Amazing job, love it

@SusiJo
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SusiJo commented Jul 13, 2022

Thanks @maxulysse for reviewing!

FriederikeHanssen
FriederikeHanssen approved these changes Jul 13, 2022
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great work, I can take a more detailed look still if you want, but looks really good

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@FriederikeHanssen
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@SusiJo since these are quite significant changes did you also run the mnaul tests locally?

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SusiJo commented Jul 14, 2022 •
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Yes, i ran almost all test cases locally, including all manual tests. I'm just wondering about strelkakb with manta and strelka together. Before applying the prefix changes, the strelka was using the manta output. Now both produce outputs 🤔

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The PR looks almost ready to be merged. I couldn’t find anything obvious.

@maxulysse maxulysse merged commit 5949d5f into nf-core:dev Jul 14, 2022
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@maxulysse maxulysse maxulysse approved these changes

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@SusiJo @maxulysse @FriederikeHanssen