Added cnvkit for tumor_only#545
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FriederikeHanssen merged 12 commits intonf-core:devfrom May 30, 2022
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Note: the module |
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Looks really good already. Just want to clear up the crai thing before merging
| - [#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
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| 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
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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PR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).