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Updating yml
[arvados-tutorial.git]
/
cwl
/
gatk-haplotypecaller.cwl
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cwlVersion: v1.1
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class: CommandLineTool
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label: Germline variant calling using GATK with output gvcf
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requirements:
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DockerRequirement:
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dockerPull: broadinstitute/gatk
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InitialWorkDirRequirement:
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listing:
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- $(inputs.bam)
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hints:
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ResourceRequirement:
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ramMin: 10000
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coresMin: 4
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inputs:
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bam:
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type: File
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secondaryFiles:
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- .bai
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reference:
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type: File
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secondaryFiles:
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- .amb
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- .ann
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- .bwt
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- .pac
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- .sa
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- .fai
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- ^.dict
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sample: string
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outputs:
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gvcf:
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type: File
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outputBinding:
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glob: "*vcf.gz"
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arguments:
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- java
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- -jar
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- /gatk/gatk.jar
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- HaplotypeCaller
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- -R
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- $(inputs.reference)
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- -I
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- $(inputs.bam)
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- -O
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- $(runtime.outdir)/$(inputs.sample).gatk.g.vcf.gz
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- -ERC
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- "GVCF"