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DataBiosphere / analysis_pipeline_WDL

Collection of WDL workflows based off the University of Washington TOPMed DCC Best Practices for GWAS. The WDL structure was based upon CWLs written by the Seven Bridges development team.
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[assoc-agg] Prepare segments drops chrX #66

Closed aofarrel closed 2 years ago

aofarrel commented 2 years ago

Although it does not error out as it did previously (https://github.com/DataBiosphere/analysis_pipeline_WDL/issues/65), it does fail to output chrX-related files.

aofarrel commented 2 years ago

Checked an old run on SB... a run of chr1, chr2, and chrX does not result in chrX getting dropped. It's clearly still there for assoc_combine_r. So this is a divergence.