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mc3_vcf2maf_full.cwl
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mc3_vcf2maf_full.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement
inputs:
tumorID:
type: string
normalID:
type: string
tumor:
type: File
normal:
type: File
bed_file:
type: File?
centromere:
type: File
cosmic:
type: File
dbsnp:
type: File
refFasta:
type: File
vepData:
type: Directory
markSamples:
type: Directory
markVariants:
type: Directory
steps:
call_variants:
run: mc3_variant.cwl
in:
tumor: tumor
normal: normal
centromere: centromere
bed_file: bed_file
cosmic: cosmic
dbsnp: dbsnp
reference: refFasta
tumorID: tumorID
normalID: normalID
out:
- pindelVCF
- somaticsniperVCF
- varscansVCF
- varscaniVCF
- museVCF
- mutectVCF
- radiaVCF
- indelocatorVCF
convert:
run: mc3_vcf2maf.cwl
in:
normalID: normalID
tumorID: tumorID
museVCF: call_variants/museVCF
mutectVCF: call_variants/mutectVCF
somaticsniperVCF: call_variants/somaticsniperVCF
varscansVCF: call_variants/varscansVCF
varscaniVCF: call_variants/varscaniVCF
radiaVCF: call_variants/radiaVCF
pindelVCF: call_variants/pindelVCF
indelocatorVCF: call_variants/indelocatorVCF
refFasta: refFasta
vepData: vepData
tumor_bam_name:
source: tumor
valueFrom: $(self.basename)
normal_bam_name:
source: normal
valueFrom: $(self.basename)
out:
- outmaf
markfiles:
run: markfiles.cwl
in:
sampleID: tumorID
mergedMAF: convert/outmaf
markSamples: markSamples
markVariants: markVariants
out:
- markedMAF
outputs:
outmaf:
type: File
outputSource: markfiles/markedMAF