projects
/
arvados-tutorial.git
/ blob
b1e9373b008ea868185e7ed1a4779f82d6b84fe6
[arvados-tutorial.git]
/
cwl
/
helper
/
calc-coverage.cwl
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cwlVersion: v1.1
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class: CommandLineTool
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label: Marking Duplicates using Picard
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requirements:
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DockerRequirement:
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dockerPull: broadinstitute/gatk
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hints:
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ResourceRequirement:
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ramMin: 20000
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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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outputs:
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dupbam:
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type: File
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outputBinding:
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glob: "*.bam"
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dupmetrics:
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type: File
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outputBinding:
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glob: "*.txt"
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baseCommand: /gatk/gatk
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arguments:
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- "--java-options"
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- "-Xmx8G"
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- MarkDuplicates
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- prefix: "-I"
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valueFrom: $(inputs.bam.path)
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- prefix: "-O"
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valueFrom: marked_dups$(inputs.bam.basename)
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- prefix: "-M"
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valueFrom: "metrics.txt"