Containerize and write CWL for GATK 4 BaseQualityScoreRecalibrator

mskcc / cwl-commandlinetools

Central location for CWL CommandLineTools

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Containerize and write CWL for GATK 4 BaseQualityScoreRecalibrator #30

Closed rhshah closed 5 years ago

rhshah commented 5 years ago

Tool: GATK BaseQualityScoreRecalibrator Location: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_bqsr_BaseRecalibrator.php GATK Version: 4.1.2

[x] Container
[x] CWL
[x] Run Test

shalabhsuman commented 5 years ago

Having error while utilizing the --java-options "-Xmx4G" with an error Could not find or load main class "-Xmx4G". I have temporarily deactivated this parameter until we figure out a resolution. GH-31

[ ] Resolved

shalabhsuman commented 5 years ago

$(inputs.input.basename.replace('.bam', '')).recal.table along with -output prefix in the Arguments inside CWL gives a warning. GH-31 @ionox0

[ ] Resolved