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broadinstitute / viral-ngs

Viral genomics analysis pipelines
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expose --skipMarkDupes for WDL align_and_plot #924

Closed dpark01 closed 5 years ago

dpark01 commented 5 years ago

The WDL plot_coverage task in tasks_reports.wdl should expose a boolean optional input parameter that passes (or doesn't pass) --skipMarkDupes to its invocation of read_utils.py align_and_fix

dpark01 commented 5 years ago

Your PR says this "addresses #924" but I think it needs to say that it "fixes" or some other magic word like that in order to auto-close the related issue.