/
sv_depth_caller_filter.cwl
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/
sv_depth_caller_filter.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Filter single sample sv vcf from depth callers(cnvkit/cnvnator)"
inputs:
deletion_depth:
type: double?
duplication_depth:
type: double?
reference:
type: string
min_sv_size:
type: int?
output_vcf_name:
type: string?
sv_vcf:
type: File
vcf_source:
type:
- type: enum
symbols: ["cnvkit", "cnvnator"]
outputs:
filtered_vcf:
type: File
outputSource: filtered_vcf_index/indexed_vcf
steps:
size_filter:
run: ../tools/filter_sv_vcf_size.cwl
in:
input_vcf: sv_vcf
size_method:
default: "min_len"
sv_size: min_sv_size
out:
[filtered_sv_vcf]
depth_filter:
run: ../tools/filter_sv_vcf_depth.cwl
in:
input_vcf: size_filter/filtered_sv_vcf
deletion_depth: deletion_depth
duplication_depth: duplication_depth
output_vcf_name: output_vcf_name
vcf_source: vcf_source
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]