projects
/
arvados-tutorial.git
/ blob
30857f46e7eaeb1cfa285d16dc1bff19b786ddfb
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
report-wf.cwl
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cwlVersion: v1.1
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class: Workflow
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label: Report generation workflow
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inputs:
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gvcf:
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type: File
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samplename:
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type: string
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clinvarvcf:
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type: File
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reportfunc:
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type: File
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headhtml:
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type: File
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tailhtml:
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type: File
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outputs:
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report:
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type: File
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outputSource: generate-report/report
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steps:
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gvcf-to-vcf:
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run: gvcf-to-vcf.cwl
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in:
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gvcf: gvcf
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samplename: samplename
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out: [vcf]
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annotate:
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run: annotate-vcf.cwl
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in:
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vcf: gvcf-to-vcf/vcf
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clinvarvcf: clinvarvcf
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out: [reporttxt]
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generate-report:
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run: generate-report.cwl
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in:
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reportfunc: reportfunc
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sampletxt: annotate/reporttxt
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headhtml: headhtml
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tailhtml: tailhtml
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out: [report]