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docm_cle.cwl
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docm_cle.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Detect Docm variants"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
tumor_bam:
type: File
secondaryFiles: [^.bai]
normal_bam:
type: File
secondaryFiles: [^.bai]
docm_vcf:
type: File
secondaryFiles: [.tbi]
interval_list:
type: File
filter_docm_variants:
type: boolean
outputs:
docm_variants_vcf:
type: File
outputSource: index2/indexed_vcf
secondaryFiles: [.tbi]
steps:
GATK_haplotype_caller:
run: ../tools/docm_gatk_haplotype_caller.cwl
in:
reference: reference
bam: tumor_bam
normal_bam: normal_bam
docm_vcf: docm_vcf
interval_list: interval_list
out:
[docm_raw_variants]
bgzip:
run: ../tools/bgzip.cwl
in:
file: GATK_haplotype_caller/docm_raw_variants
out:
[bgzipped_file]
index:
run: ../tools/index_vcf.cwl
in:
vcf: bgzip/bgzipped_file
out:
[indexed_vcf]
decompose:
run: ../tools/vt_decompose.cwl
in:
vcf: index/indexed_vcf
out:
[decomposed_vcf]
docm_filter:
run: ../tools/filter_vcf_docm.cwl
in:
docm_raw_variants: decompose/decomposed_vcf
normal_bam: normal_bam
tumor_bam: tumor_bam
filter_docm_variants: filter_docm_variants
out:
[docm_filtered_variants]
bgzip2:
run: ../tools/bgzip.cwl
in:
file: docm_filter/docm_filtered_variants
out:
[bgzipped_file]
index2:
run: ../tools/index_vcf.cwl
in:
vcf: bgzip2/bgzipped_file
out:
[indexed_vcf]