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Add cnvkit germline mode#576

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maxulysse merged 20 commits intonf-core:devfrom
SusiJo:cnvkit_germline
Jun 7, 2022
Merged

Add cnvkit germline mode#576
maxulysse merged 20 commits intonf-core:devfrom
SusiJo:cnvkit_germline

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@SusiJo SusiJo commented Jun 1, 2022

PR checklist

This PR implements germline variant calling with cnvkit.

  • 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).

@SusiJo SusiJo requested a review from maxulysse as a code owner June 1, 2022 16:06
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SusiJo commented Jun 1, 2022

Please note that the new upstream nf-core/modules cnvkit/batch has to be installed after the PR to modules is merged.

maxulysse
maxulysse reviewed Jun 2, 2022
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Comment thread subworkflows/local/germline_variant_calling.nf Outdated
maxulysse
maxulysse reviewed Jun 2, 2022
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Comment thread subworkflows/local/germline_variant_calling.nf Outdated
maxulysse
maxulysse reviewed Jun 2, 2022
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LGTM

FriederikeHanssen
FriederikeHanssen reviewed Jun 3, 2022
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Looks great, only thing missing would be some CI tests. 🚀

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maxulysse commented Jun 3, 2022

@SusiJo you can run prettier with @nf-core-bot fix linting

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SusiJo commented Jun 3, 2022

Ah cool! Good to know for next time :D

maxulysse
maxulysse reviewed Jun 3, 2022
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Comment thread subworkflows/local/germline_variant_calling.nf Outdated
@SusiJo @maxulysse
Update subworkflows/local/germline_variant_calling.nf
2eb63ce 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
maxulysse
maxulysse approved these changes Jun 3, 2022
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<3

FriederikeHanssen
FriederikeHanssen reviewed Jun 3, 2022
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Comment thread tests/test_tools.yml
- path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.cnr
- path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.cns
- path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.call.cns

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looks great, thanks for adding those <3

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maxulysse commented Jun 3, 2022

CI tests are badly failing

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FriederikeHanssen commented Jun 3, 2022

linting fails for cnvkit bathc:

│ cnvkit/batch                              │ modules/nf-co… │ Local copy of   │
│                                           │                │ module does not │
│                                           │                │ match remote

could that be the reason?

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maxulysse commented Jun 3, 2022

Seems likely, anyway error message is not helping as usual...

@maxulysse maxulysse merged commit 205b33f into nf-core:dev Jun 7, 2022
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@SusiJo @maxulysse @FriederikeHanssen
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