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cwlVersion: v1.0
class: Workflow
inputs:
rawRadia:
type: File
rawVarscans:
type: File
rawSomsniper:
type: File
rawMuse:
type: File
rawPindel:
type: File
rawIndelocator:
type: File
tumor:
type: File
normal:
type: File
reference:
type: File
tumorID:
type: string
normalID:
type: string
steps:
filterRadia:
run: ./tools/radia-tool/radia_filter.cwl
in:
inputVCF: rawRadia
tumor: tumor
normal: normal
patientId:
default: tumorID
reference: reference
out:
- mutations
fpfilterSomaticSniper:
run: ./tools/fpfilter-tool/fpfilter.cwl.yaml
in:
vcf-file: rawSomsniper
bam-file: tumor
reference: reference
output:
default: somatic_sniper_fpfilter.vcf
out:
- filtered_vcf
fpfilterVarscans:
run: ./tools/fpfilter-tool/fpfilter.cwl.yaml
in:
vcf-file: rawVarscans
bam-file: tumor
reference: reference
output:
default: varscan_fpfilter.vcf
out:
- filtered_vcf
filterMuse:
run: ./tools/muse-tool/muse.filter.cwl
in:
vcf: rawMuse
output_name:
default: muse_filtered.vcf
out:
- output_vcf
filterPindel:
run: ./tools/vcf-tools/filter_vcf.cwl
in:
vcf: rawPindel
output_name:
default: pindel_filtered.vcf
cutoff:
default: 3
out:
- output_vcf
filterIndelocator:
run: tools/vcf-tools/filter_vcf.cwl
in:
vcf: rawIndelocator
output_name:
default: indelocator_filtered.vcf
cutoff:
default: 3
tumorID: tumorID
normalID: normalID
out:
- output_vcf
outputs:
filteredRadiaVCF:
type: File
outputSource:
filterRadia/mutations
fpfilteredSomaticsniperVCF:
type: File
outputSource:
fpfilterSomaticSniper/filtered_vcf
fpfilteredVarscansVCF:
type: File
outputSource:
fpfilterVarscans/filtered_vcf
filteredMuseVCF:
type: File
outputSource:
filterMuse/output_vcf
filteredPindelVCF:
type: File
outputSource:
filterPindel/output_vcf
filteredIndelocatorVCF:
type: File
outputSource:
filterIndelocator/output_vcf
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