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Added cnvkit for tumor_only #545

Merged
merged 12 commits into from
May 30, 2022
Merged

Added cnvkit for tumor_only #545

merged 12 commits into from
May 30, 2022

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SusiJo
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@SusiJo SusiJo commented May 13, 2022

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).

@SusiJo
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SusiJo commented May 13, 2022

Note: the module cnvkit/batch needs to be adjusted and needs to test if normal samples are provided.
Also, the new local modules should probably be implemented in nf-core/modules and should be removed here later.

@SusiJo SusiJo marked this pull request as ready for review May 25, 2022 07:33
@SusiJo SusiJo requested a review from maxulysse as a code owner May 25, 2022 07:33
FriederikeHanssen
FriederikeHanssen reviewed May 29, 2022
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Looks really good already. Just want to clear up the crai thing before merging

CHANGELOG.md
@@ -73,7 +74,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#513](https://github.com/nf-core/sarek/pull/513), [#527](https://github.com/nf-core/sarek/pull/527) - CNV is back
- [#529](https://github.com/nf-core/sarek/pull/529) - Do not save `versions.yml` files
- [#524](https://github.com/nf-core/sarek/pull/524) - Fix intervals usage by counting the actual list of scatter/gather files produced and not overall number of intervals
- [#549](https://github.com/nf-core/sarek/pull/549) - Fix unique lanes required for Freebayes: issue [#311](https://github.com/nf-core/sarek/issues/311), replaces `meta.clone()` with actual copy of map to avoid issues with https://nfcore.slack.com/archives/C027CM7P08M/p1644241819942339
- [#549](https://github.com/nf-core/sarek/pull/549) - Fix unique lanes required for Freebayes: issue [#311](https://github.com/nf-core/sarek/issues/311), replaces `meta.clone()` with actual copy of map to avoid issues with <https://nfcore.slack.com/archives/C027CM7P08M/p1644241819942339>
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bit confused this is part of the PR 🤔

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just prettier being prettier

conf/modules.config Outdated Show resolved Hide resolved
subworkflows/local/tumor_variant_calling.nf
@@ -83,6 +84,20 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
ch_versions = ch_versions.mix(RUN_CONTROLFREEC_TUMORONLY.out.versions)
}

if(tools.contains('cnvkit')){
cram_recalibrated_cnvkit = cram_recalibrated
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same here about the crai

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all good, samtools computes the bai index, so this is all fine

SusiJo and others added 2 commits May 30, 2022 09:16
@SusiJo @FriederikeHanssen
rm line update conf/modules.config
d81aef0 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@SusiJo
adjusted whitespaces
918e841
@FriederikeHanssen FriederikeHanssen self-requested a review May 30, 2022 07:32
FriederikeHanssen
FriederikeHanssen approved these changes May 30, 2022
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🚀

@FriederikeHanssen FriederikeHanssen merged commit c13baa8 into nf-core:dev May 30, 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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@SusiJo @FriederikeHanssen