assoc prepare segments task errors out on non-autosomes

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.

6 stars 3 forks source link

assoc prepare segments task errors out on non-autosomes #65

Closed aofarrel closed 2 years ago

aofarrel commented 2 years ago

Traceback (most recent call last): File "assoc-aggregate/prepare_segments_1.py", line 62, in input_gdss = pair_chromosome_gds(IIinput_gds_filesII) File "assoc-aggregate/prepare_segments_1.py", line 45, in pair_chromosome_gds gdss[int(find_chromosome(file_array[i]))] = os.path.basename(file_array[i]) ValueError: invalid literal for int() with base 10: 'X'

aofarrel commented 2 years ago

Verified fixed on Terra here: https://github.com/DataBiosphere/analysis_pipeline_WDL/pull/58/commits/63e0cf183f14eb91c2a8dffc882f376a9d64b0c7