The ploidy_table is an intermediate output in the JoinRawCalls workflow but is necessary for further downstream analysis. This file is required for further downstream analysis and is a necessary input for FilterGenotypes. Thus it should be a final output of the workflow.
The JoinRawCalls.wdl has been modified to make the ploidy table generated by calling CreatePloidyTableFromPed from the TasksClusterBatch.wdl a final output of the entire wdl.
This passed validation with both womtool and cromshell against the reference panel. This addresses issue #636 [https://github.com/broadinstitute/gatk-sv/issues/636#issue-2119378008].
The ploidy_table is an intermediate output in the JoinRawCalls workflow but is necessary for further downstream analysis. This file is required for further downstream analysis and is a necessary input for FilterGenotypes. Thus it should be a final output of the workflow. The JoinRawCalls.wdl has been modified to make the ploidy table generated by calling CreatePloidyTableFromPed from the TasksClusterBatch.wdl a final output of the entire wdl. This passed validation with both womtool and cromshell against the reference panel. This addresses issue #636 [https://github.com/broadinstitute/gatk-sv/issues/636#issue-2119378008].