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Updating cwl
[arvados-tutorial.git]
/
cwl
/
bwamem-samtools-view.cwl
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cwlVersion: v1.1
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class: CommandLineTool
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label: Realigning fastqs and converting output to bam
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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: 26000
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coresMin: 8
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inputs:
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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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fastq1: File
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fastq2: File
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sample: string
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stdout: $(inputs.sample).bam
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outputs:
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bam:
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type: File
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outputBinding:
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glob: "*bam"
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arguments:
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- /bwa-0.7.17/bwa
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- mem
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- -t
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- $(runtime.cores)
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- $(inputs.reference)
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- -R
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- "@RG\\tID:sample\\tSM:sample\\tLB:sample\\tPL:ILLUMINA"
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- $(inputs.fastq1)
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- $(inputs.fastq2)
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- shellQuote: false
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valueFrom: '|'
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- samtools
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- view
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- -b
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- -S
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- shellQuote: false
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valueFrom: '-'