This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
bcbio configuration file (bcbio_system.yaml)
I have a question regarding how to tune options for specific software (gatk) in bcbio conf file (bcbio_system.yaml).
I want to define GATK PrintReads java memory parameters Xmx like this:
resources: gatk-printreads: jvm_opts: ["-Xmx7000m"]
However, I am not sure if this is the right way to do it, is "gatk-printreads" the right parameter? Or how do I specifically define java options for PrintReads in config file?
I am running bcbio-nextgen 1.0.5 with GATK 3.8.