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Sydney-Informatics-Hub / Somatic-ShortV

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GATK Module Load Missing In Rerun Script #8

Closed DarioS closed 2 years ago

DarioS commented 3 years ago

https://github.com/Sydney-Informatics-Hub/Somatic-ShortV/blob/8bcd9da640733ad4dd9c4b55f8e95c75a9694513/gatk4_getpileupsummaries_missing_run_parallel.pbs#L43-L46

There ought to be a module load gatk/4.1.2.0 here somewhere.

DarioS commented 3 years ago

Same for gatk4_calculatecontamination_run_parallel.pbs (which is also missing any mention in the user guide).

georgiesamaha commented 2 years ago

Have added missing gatk modules to both scripts, thanks for pointing them out Dario. Will also update the documentation