Refactor postvariantcalling. Split out valrociraptor vs other options #2043
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Waiting for conlcusion on discussion here before updating all the checksums: https://nfcore.slack.com/archives/C05V9FRJYMV/p1761906884846409?thread_ts=1761564791.923049&cid=C05V9FRJYMV |
| // Set Varlociraptor reference files | ||
| varlociraptor_scenario_germline = params.varlociraptor_scenario_germline ? Channel.fromPath(params.varlociraptor_scenario_germline).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : Channel.fromPath("${projectDir}/assets/varlociraptor_germline.yte.yaml").collect() | ||
| varlociraptor_scenario_somatic = params.varlociraptor_scenario_somatic ? Channel.fromPath(params.varlociraptor_scenario_somatic).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : Channel.fromPath("${projectDir}/assets/varlociraptor_somatic.yte.yaml").collect() | ||
| varlociraptor_scenario_tumor_only = params.varlociraptor_scenario_tumor_only ? Channel.fromPath(params.varlociraptor_scenario_tumor_only).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : Channel.fromPath("${projectDir}/assets/varlociraptor_tumor_only.yte.yaml").collect() |
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Can we put that directly on the call to Sarek workflow?
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as you wish, thought it would be more new syntaxy to do it in the main?
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basically this follows where currently the intervals and annotation files are defined.
| { assert snapshot( | ||
| workflow.out.vcfs, | ||
| workflow.out.tbis, | ||
| workflow.out.versions |
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Can we capture the yaml output instead?
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for the versions?
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hold on what is the difference? this just snapshots the yaml, isn't that what we want? got an example of what you want instead?
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Previously, the post-variant calling logic allowed mixing different post-processing strategies (varlociraptor,
normalization, concatenation) in confusing ways. The main workflow had complex conditional logic to determine which VCFs was used based on what post-processing was requested, a lot of computation was repeated on both raw and post-processed variants. This made the data flow hard to follow and error-prone.
Changes
Enforced either-or logic in post-variant calling:
Simplified main workflow:
Additional improvements:
Resume limitations with varlociraptor
While the overall data flow is cleaner, varlociraptor is currently not reliable resuming. I marked the likely location where this occurs but it is currently not clear to me why.