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mutect.cwl
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mutect.cwl
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cwlVersion: v1.0
class: CommandLineTool
doc: "Mutect 1.1.5"
hints:
DockerRequirement:
dockerPull: quay.io/opengenomics/mutect
baseCommand: ['python', '/opt/mutect.py']
inputs:
tumor:
type: File
inputBinding:
prefix: --input_file:tumor
normal:
type: File
inputBinding:
prefix: --input_file:normal
reference:
type: File
inputBinding:
prefix: --reference_sequence
cosmic:
type: File?
inputBinding:
prefix: --cosmic
dbsnp:
type: File?
inputBinding:
prefix: --dbsnp
secondaryFiles: .tbi
tumor_lod:
type: float?
default: 6.3
inputBinding:
prefix: --tumor_lod
initial_tumor_lod:
type: float?
default: 4.0
inputBinding:
prefix: --initial_tumor_lod
ncpus:
type: int?
inputBinding:
position: 2
prefix: --ncpus
out:
type: string?
default: call_stats.txt
inputBinding:
prefix: --out
coverage_file:
type: string?
default: coverage.wig.txt
inputBinding:
prefix: --coverage_file
vcf:
type: string?
default: mutations.vcf
inputBinding:
prefix: --vcf
outputs:
coverage:
type: File
outputBinding:
glob: $(inputs.coverage_file)
call_stats:
type: File
outputBinding:
glob: $(inputs.out)
mutations:
type: File
outputBinding:
glob: $(inputs.vcf)