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|
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
id: "merge_vcfs"
label: "merge_vcfs"
doc: |
This tool will merge VCFs by type (SV, SNV, INDEL). This CWL wrapper was written by Solomon Shorser.
The Perl script was originaly written by Brian O'Connor and maintained by Solomon Shorser.
$namespaces:
s: https://schema.org/
$schemas:
- https://schema.org/version/latest/schemaorg-current-https.rdf
s:author:
s:name: "Solomon Shorser"
s:email: "solomon.shorser@oicr.on.ca"
requirements:
- class: DockerRequirement
dockerPull: quay.io/pancancer/pcawg-oxog-tools
- class: InlineJavascriptRequirement
expressionLib:
- { $include: vcf_merge_util.js }
inputs:
- id: "#broad_snv"
type: File[]
- id: "#sanger_snv"
type: File[]
- id: "#de_snv"
type: File[]
- id: "#muse_snv"
type: File[]
- id: "#broad_sv"
type: File[]
- id: "#sanger_sv"
type: File[]
- id: "#de_sv"
type: File[]
- id: "#broad_indel"
type: File[]
- id: "#sanger_indel"
type: File[]
- id: "#de_indel"
type: File[]
- id: "#smufin_indel"
type: File[]
- id: "#out_dir"
type: string
inputBinding:
position: 12
prefix: --outdir
outputs:
output:
type:
type: array
items: File
outputBinding:
glob: "*.clean.sorted.vcf.gz"
arguments:
- prefix: --broad_snv
valueFrom: $(formatArray(inputs.broad_snv))
- prefix: --sanger_snv
valueFrom: $(formatArray(inputs.sanger_snv))
- prefix: --dkfz_embl_snv
valueFrom: $(formatArray(inputs.de_snv))
- prefix: --muse_snv
valueFrom: $(formatArray(inputs.muse_snv))
- prefix: --broad_sv
valueFrom: $(formatArray(inputs.broad_sv))
- prefix: --sanger_sv
valueFrom: $(formatArray(inputs.sanger_sv))
- prefix: --dkfz_embl_sv
valueFrom: $(formatArray(inputs.de_sv))
- prefix: --broad_indel
valueFrom: $(formatArray(inputs.broad_indel))
- prefix: --sanger_indel
valueFrom: $(formatArray(inputs.sanger_indel))
- prefix: --dkfz_embl_indel
valueFrom: $(formatArray(inputs.de_indel))
- prefix: --smufin_indel
valueFrom: $(formatArray(inputs.smufin_indel))
baseCommand: /opt/oxog_scripts/vcf_merge_by_type.pl
|
