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mskcc / cwl-commandlinetools

Central location for CWL CommandLineTools
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Containerize and write CWL for GATK4 ApplyBQSR #32

Closed shalabhsuman closed 5 years ago

shalabhsuman commented 5 years ago

Tool: GATK4 ApplyBQSR (~GATK3 PrintReads) Location: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_bqsr_ApplyBQSR.php Version: 4.1.2.0

shalabhsuman commented 5 years ago

Have to check the usage of --java-options "-Xmx4G" but the tool works without it. so have temporarily deactivated that argument.

shalabhsuman commented 5 years ago

Enabling the --emit-original-quals option by using default: 'true' inside CWL