Keep unresolved Manta calls #723
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Have TinyResolve output tar files of tloc and unresolved Manta calls instead of arrays of files.
Update GatherBatchEvidence to match the output names of TinyResolve.
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The PR has changed significantly since the approval so it should be rechecked. The TinyResolve workflow has been tested, but not any calling workflows. |
Co-authored-by: Mark Walker <[email protected]>
TinyResolve produces tar files with a top level directory and all VCFs inside the directory. However, the ClusterBatch workflow expects tar files with all VCFs placed at the top level. This commit updates the TinyResolve workflow to produce tar files with all VCFs at the top level to be compatible with ClusterBatch.
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GATK's SVCluster tool will not accept all SV type / CPX subtype combinations so we remove the CPX subtype annotation from all non-CPX SVs in the VCFs produced by TinyResolve.
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Keep unresolved Manta calls in TinyResolve to assist with resolving ultra complex events.