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cnv.cwl
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cnv.cwl
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#!/usr/bin/env cwl-runner
#
class: Workflow
cwlVersion: v1.0
doc: "Copynumber variation workflow, runs ADTEx and Varscan"
requirements:
- class: MultipleInputFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
inputs:
TUMOR_BAM: File
NORMAL_BAM: File
SAMPLE_ID: string
CENTROMERES: File
TARGETS: File
GENO_FA_GZ: File
outputs:
VARSCAN_OUTCNV:
type: File
outputSource: varscan/output
ADTEX_OUTCNV:
type: File
outputSource: adtex/output
steps:
zcat:
run: zcat.cwl
in:
gzipFile: GENO_FA_GZ
unzippedFileName:
valueFrom: $('genome.fa')
out: [unzippedFile]
varscan:
run: varscan_cnv.cwl
in:
control_bam_input: NORMAL_BAM
tumor_bam_input: TUMOR_BAM
targets: TARGETS
centromeres: CENTROMERES
sample_id: SAMPLE_ID
genome: zcat/unzippedFile
out:
[output]
adtex:
run: adtex.cwl
in:
control_bam_input: NORMAL_BAM
tumor_bam_input: TUMOR_BAM
targets: TARGETS
centromeres: CENTROMERES
sample_id: SAMPLE_ID
out:
[output]