15 implement cancer predisposition sequencing reporter#68
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15 implement cancer predisposition sequencing reporter#68
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@famosab I'm a little bit scared on how to deal with all this pull request at the same time 😨 |
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ToDo:
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Todo:
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Undo concat because we need a sort of consensus approach that needs to be discussed and is beyond the scope of this PR |
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| conda "${moduleDir}/environment.yml" | ||
| container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container | ||
| ? 'docker.io/sigven/pcgr:2.2.1' |
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Don't think you need the ternary here ;-)
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True, I would like to keep it as reminder that we want distinct containers here at some point. Is that ok?
| If you have multiple VCFs for the same sample (e.g. one per caller), provide one row per VCF. The pipeline will keep caller-specific files separate during preprocessing and then consolidate/intersect somatic calls per sample for PCGR reporting. | ||
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| > [!NOTE] | ||
| > Intersection of calls is only implemented for the somatic reporting. For germline calls please provide unique sample ids, otherwise the files will be overwritten. |
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Shouldn't there be something programmatic to prevent that? Seems dangerous.
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Yes I will add a check for the samplesheet.
Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).