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bcbio configuration file (bcbio_system.yaml)

Hello!

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.

Thanks!

Tagged:

Issue · Github
by Sheila

Issue Number
2652
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Answers

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