Allow users to custom set the memory for the RevertSam task in MicrobialGenomePipeline

broadinstitute / GATK-for-Microbes

BSD 3-Clause "New" or "Revised" License

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Allow users to custom set the memory for the RevertSam task in MicrobialGenomePipeline #24

Open jason-cerrato opened 3 years ago

jason-cerrato commented 3 years ago

Users using large bam files with the MicrobialGenomePipeline run into java.lang.OutOfMemoryError with the hard-coded memory values.

Screen Shot 2021-03-17 at 3 15 23 PM

Having the ability to set a custom -Xmx value for the Java command and a custom value for the task's memory configuration will enable users using large bams to use the pipeline without having to re-write the WDL.