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adding base recalibrator yml and updating bwamem yml
[arvados-tutorial.git]
/
cwl
/
samtools-index.cwl
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cwlVersion: v1.1
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class: CommandLineTool
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$namespaces:
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arv: "http://arvados.org/cwl#"
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cwltool: "http://commonwl.org/cwltool#"
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requirements:
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DockerRequirement:
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dockerPull: curii/bwa-samtools-picard
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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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arv:RuntimeConstraints:
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outputDirType: keep_output_dir
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inputs:
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bam: File
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outputs:
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out:
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type: File
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outputBinding:
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glob: "*bam"
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secondaryFiles:
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- .bai
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baseCommand: samtools
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arguments:
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- index
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- $(inputs.bam.basename)