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mskcc / pluto-cwl

CWL workflows for helix filter scripts
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fix duplicate file output in portal workflow #101

Closed stevekm closed 2 years ago

stevekm commented 2 years ago

portal_cna_data_file and merged_cna_file are being output with the same filename (data_CNA.txt) which is causing one file or the other to get automatically renamed by cwltool / Toil

this is breaking test cases that expect both files to be named data_CNA.txt

in most test cases these two files also end up with the same sha1 hash so they are identical files

Need to figure out what the handling method for this should be

stevekm commented 2 years ago

related to #92 since this will potentially break Jenkins test cases as well

stevekm commented 2 years ago

I think this is fixed?