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oxog.cwl
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#!/usr/bin/env cwl-runner
#run as: dockstore --debug tool launch --descriptor cwl --local-entry --entry ./oxog.cwl --json oxog_tool_input.json
cwlVersion: v1.0
class: CommandLineTool
doc: |
This tool will run OxoG. The OxoG tool was written by Dimitri Livitz. This CWL wrapper was written by Solomon Shorser.
# Input file should look like this:
# {
# "oxoQScore":10.5,
# "tumourID":"123456789",
# "inputFileDirectory" : {
# "class":"Directory",
# "path":"/media/sshorser/Data/oxog_test_data",
# "location":"/media/sshorser/Data/oxog_test_data"
# },
# "tumourBamFilename" : "f5c9381090a53c54358feb2ba5b7a3d7.bam",
# "tumourBamIndexFilename" : "f5c9381090a53c54358feb2ba5b7a3d7.bam.bai",
# "vcfNames": [
# "f7b84c09-15d4-3046-e040-11ac0c4847ff.svcp_1-0-3.20150120.somatic.snv_mnv.cleaned.vcf.gz",
# "f7b84c09-15d4-3046-e040-11ac0c4847ff.dkfz-snvCalling_1-0-132-1.20150626.somatic.snv_mnv.cleaned.vcf.gz",
# "f7b84c09-15d4-3046-e040-11ac0c4847ff.broad-mutect-v3.20160222.somatic.snv_mnv.cleaned.vcf.gz"
# ],
# "refDataDir": {
# "class":"Directory",
# "path":"/datastore/oxog_refdata",
# "location":"/datastore/oxog_refdata"
# }
# }
dct:creator:
foaf:name: "Solomon Shorser"
foaf:mbox: "[email protected]"
requirements:
- class: DockerRequirement
dockerPull: quay.io/pancancer/pcawg-oxog-filter
- class: InlineJavascriptRequirement
inputs:
- id: inputFileDirectory
type: Directory
inputBinding:
position: 0
prefix: --inputDir
- id: tumourID
type: string
inputBinding:
position: 1
prefix: --pairID
- id: tumourBamFilename
type: File
inputBinding:
position: 2
prefix: --bamName
secondaryFiles: ".bai"
- id: oxoQScore
type: float
inputBinding:
position: 4
prefix: --oxoqScore
- id: vcfNames
type: File[]
inputBinding:
position: 5
prefix: --vcfs
# secondaryFiles:
# - ".tbi"
- id: refDataDir
type: Directory
inputBinding:
position: 7
prefix: --refDataDir
outputs:
debuggingOutput:
type: File
outputBinding:
glob: "failing_intermediates.tar"
oxogVCF:
type: File[]
outputBinding:
glob: "output_files/*oxoG.vcf.gz"
oxogTBI:
type: File[]
outputBinding:
glob: "output_files/*oxoG.vcf.gz.tbi"
oxogMAF:
type: File
outputBinding:
glob: "output_files/*oxoG.maf"
oxogSupplementaryFile:
type: File
outputBinding:
glob: "output_files/*oxoG.supplementary.tar.gz"
usageInfo:
type: File
outputBinding:
glob: "output_files/*summary.usage.txt"
baseCommand: [ python3, /cga/fh/pcawg_pipeline/run_oxog_tool.py ]