BWA-MEM2 is not configurable from modules.config

sanger-tol / treeval

Pipelines for the production of Treeval data

https://pipelines.tol.sanger.ac.uk/treeval

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BWA-MEM2 is not configurable from modules.config #304

Open DLBPointon opened 3 months ago

DLBPointon commented 3 months ago

Description of the bug

BWA-mem2 in CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT is hardcoded for the arguments -5SPCp rather than accepting args2 which is controlled via modules.config.

Command used and terminal output

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Relevant files

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System information

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yumisims commented 3 months ago

I was a bit cautious about this being extra argument, because it is needed for the IO.