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Merge branch '19997-glm'
[lightning.git]
/
cwl
/
imputation
/
get-imputedvcf.cwl
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# Copyright (C) The Lightning Authors. All rights reserved.
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#
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# SPDX-License-Identifier: AGPL-3.0
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cwlVersion: v1.1
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class: CommandLineTool
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requirements:
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ShellCommandRequirement: {}
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hints:
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DockerRequirement:
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dockerPull: vcfutil
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ResourceRequirement:
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ramMin: 5000
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inputs:
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sample: string
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vcf: File
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outputs:
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imputedvcf:
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type: File
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outputBinding:
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glob: "*.vcf.gz"
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secondaryFiles: [.tbi]
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baseCommand: zcat
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arguments:
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- $(inputs.vcf)
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- shellQuote: false
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valueFrom: "|"
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- "egrep"
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- "^#|IMP"
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- shellQuote: false
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valueFrom: "|"
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- "egrep"
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- prefix: "-v"
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valueFrom: '0\|0'
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- shellQuote: false
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valueFrom: "|"
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- "bgzip"
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- "-c"
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- shellQuote: false
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valueFrom: ">"
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- $(inputs.sample).vcf.gz
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- shellQuote: false
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valueFrom: "&&"
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- "tabix"
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- $(inputs.sample).vcf.gz