Add deepsomatic tool #1647
Add deepsomatic tool #1647
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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I like where this is going. |
Fix Changelog
| intervals_only = intervals.map { intervals, num_intervals -> [[], intervals]} | ||
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| DEEPSOMATIC(cram_normal_tumor_intervals, intervals_only, fasta, fasta_fai, [ [ id:'null' ], [] ]) |
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How does this work with multiple samples? We need to ensure that each sample is run with each interval subfile and then properly merged.
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Intervals subfiles are passed to DEEPSOMATIC process through ext.prefix parameter (this is described in conf/modules/deepsomatic.config) and then output is merged with MERGE_DEEPSOMATIC_VCF and MERGE_DEEPSOMATIC_GVCF (lines 52-53)
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minor issues with managing merge conflicts, I made suggestions |
Co-authored-by: Maxime U Garcia <[email protected]>
Co-authored-by: Maxime U Garcia <[email protected]>
This is a first version of PR to add deepsomatic capabilities into sarek pipeline. Currently this PR contains code changes only (without tests and most of metadata) and created to gather the initial feedback.
PR checklist
nf-core 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).