This PR exposes --skipMarkDupes in the WDL task plot_coverage within tasks_reports.wdl to address #924. It also exposes --plotOnlyNonDuplicates for reports.py::plot_coverage, which is only used when duplicate marking is not skipped. By default, duplicates are marked and rendered on the coverage plots created by the plot_coverage task within tasks_reports.wdl.
This PR exposes
--skipMarkDupesin the WDL taskplot_coveragewithintasks_reports.wdlto address #924. It also exposes--plotOnlyNonDuplicatesforreports.py::plot_coverage, which is only used when duplicate marking is not skipped. By default, duplicates are marked and rendered on the coverage plots created by theplot_coveragetask withintasks_reports.wdl.