projects
/
arvados-tutorial.git
/ blob
cc7c23f0535b4c0124652ea36712779cf84da702
[arvados-tutorial.git]
/
cwl
/
old
/
samtools-sort.cwl
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cwlVersion: v1.1
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class: CommandLineTool
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requirements:
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DockerRequirement:
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dockerPull: curii/bwa-samtools-picard
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ShellCommandRequirement: {}
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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: File
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sample: string
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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: "*sorted.bam"
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baseCommand: samtools
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arguments:
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- sort
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- -t
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- $(runtime.cores)
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- $(inputs.bam)
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- -o
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- $(runtime.outdir)/$(inputs.sample).sorted.bam