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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "varscan somatic workflow"
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
tumor_bam:
type: File
secondaryFiles: [^.bai]
normal_bam:
type: File
secondaryFiles: [^.bai]
roi_bed:
type: File?
strand_filter:
type: int?
min_coverage:
type: int?
min_var_freq:
type: float?
p_value:
type: float?
max_normal_freq:
type: float?
outputs:
snvs:
type: File
outputSource: somatic/snvs
indels:
type: File
outputSource: somatic/indels
somatic_hc_snvs:
type: File
outputSource: process_somatic_snvs/somatic_hc
somatic_snvs:
type: File
outputSource: process_somatic_snvs/somatic
germline_hc_snvs:
type: File
outputSource: process_somatic_snvs/germline_hc
germline_snvs:
type: File
outputSource: process_somatic_snvs/germline
loh_hc_snvs:
type: File
outputSource: process_somatic_snvs/loh_hc
loh_snvs:
type: File
outputSource: process_somatic_snvs/loh
somatic_hc_indels:
type: File
outputSource: process_somatic_indels/somatic_hc
somatic_indels:
type: File
outputSource: process_somatic_indels/somatic
germline_hc_indels:
type: File
outputSource: process_somatic_indels/germline_hc
germline_indels:
type: File
outputSource: process_somatic_indels/germline
loh_hc_indels:
type: File
outputSource: process_somatic_indels/loh_hc
loh_indels:
type: File
outputSource: process_somatic_indels/loh
steps:
somatic:
run: ../tools/varscan_somatic.cwl
in:
reference: reference
normal_bam: normal_bam
tumor_bam: tumor_bam
roi_bed: roi_bed
strand_filter: strand_filter
min_coverage: min_coverage
min_var_freq: min_var_freq
p_value: p_value
out:
[snvs, indels]
process_somatic_snvs:
run: ../tools/varscan_process_somatic.cwl
in:
variants: somatic/snvs
max_normal_freq: max_normal_freq
out:
[somatic_hc, somatic, germline_hc, germline, loh_hc, loh]
process_somatic_indels:
run: ../tools/varscan_process_somatic.cwl
in:
variants: somatic/indels
max_normal_freq: max_normal_freq
out:
[somatic_hc, somatic, germline_hc, germline, loh_hc, loh]
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