Added a boolean input do_per_sample_qc to MainVcfQc, which is set to true by default. When set to false, it does not perform per-sample QC plotting (or per-family, or per-sample benchmarking as those are dependent on the outputs of per-sample QC). This can help save money when only site-level plots are needed.
Testing
Validated all WDLs and JSONs with womtool and the Terra validation script
Tested on the reference panel with do_per_sample_qc set to false and verified that the sample-level steps did not run and only the site-level outputs were in the tarball.
Updates
Added a boolean input
do_per_sample_qcto MainVcfQc, which is set to true by default. When set to false, it does not perform per-sample QC plotting (or per-family, or per-sample benchmarking as those are dependent on the outputs of per-sample QC). This can help save money when only site-level plots are needed.Testing
do_per_sample_qcset tofalseand verified that the sample-level steps did not run and only the site-level outputs were in the tarball.