/
phase_vcf.cwl
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/
phase_vcf.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "phase VCF"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
somatic_vcf:
type: File
germline_vcf:
type: File
reference:
type: string
reference_dict:
type: File
bam:
type: File
secondaryFiles: [.bai]
outputs:
phased_vcf:
type: File
outputSource: bgzip_and_index_phased_vcf/indexed_vcf
secondaryFiles: [.tbi]
steps:
combine_variants:
run: ../tools/pvacseq_combine_variants.cwl
in:
reference: reference
germline_vcf: germline_vcf
somatic_vcf: somatic_vcf
out:
[combined_vcf]
sort:
run: ../tools/sort_vcf.cwl
in:
vcf: combine_variants/combined_vcf
reference_dict: reference_dict
out:
[sorted_vcf]
bgzip_and_index:
run: bgzip_and_index.cwl
in:
vcf: sort/sorted_vcf
out:
[indexed_vcf]
phase_vcf:
run: ../tools/read_backed_phasing.cwl
in:
reference: reference
bam: bam
vcf: bgzip_and_index/indexed_vcf
out:
[phased_vcf]
bgzip_and_index_phased_vcf:
run: bgzip_and_index.cwl
in:
vcf: phase_vcf/phased_vcf
out:
[indexed_vcf]