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sv_paired_read_caller_filter.cwl
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sv_paired_read_caller_filter.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Filter single sample sv vcf from paired read callers(Manta/Smoove)"
inputs:
abundance_percentage:
type: double?
bam:
type: File
deletion_depth:
type: double?
duplication_depth:
type: double?
output_vcf_name:
type: string?
reference:
type: string
snps_vcf:
type: File?
sv_paired_count:
type: int?
sv_split_count:
type: int?
sv_vcf:
type: File
vcf_source:
type:
- type: enum
symbols: ["manta", "smoove"]
outputs:
filtered_vcf:
type: File
outputSource: filtered_vcf_index/indexed_vcf
steps:
read_support_filter:
run: ../tools/filter_sv_vcf_read_support.cwl
in:
abundance_percentage: abundance_percentage
input_vcf: sv_vcf
paired_count: sv_paired_count
split_count: sv_split_count
vcf_source: vcf_source
out:
[filtered_sv_vcf]
duphold_annotate:
run: ../tools/duphold.cwl
in:
bam: bam
reference: reference
snps_vcf: snps_vcf
sv_vcf: read_support_filter/filtered_sv_vcf
out:
[annotated_sv_vcf]
depth_filter:
run: ../tools/filter_sv_vcf_depth.cwl
in:
input_vcf: duphold_annotate/annotated_sv_vcf
deletion_depth: deletion_depth
duplication_depth: duplication_depth
output_vcf_name: output_vcf_name
vcf_source:
default: "duphold"
out:
[filtered_sv_vcf]
filtered_vcf_bgzip:
run: ../tools/bgzip.cwl
in:
file: depth_filter/filtered_sv_vcf
out: [bgzipped_file]
filtered_vcf_index:
run: ../tools/index_vcf.cwl
in:
vcf: filtered_vcf_bgzip/bgzipped_file
out:
[indexed_vcf]