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tcga-vcf-reheader.cwl
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cwlVersion: v1.0
class: CommandLineTool
label: tcga-vcf-reheader
baseCommand: ["bash", "/opt/reheader_wrapper.sh"]
requirements:
- class: DockerRequirement
dockerPull: opengenomics/tcgavcf-tool:latest
- class: InitialWorkDirRequirement
listing: [ $(inputs.varscani_vcf), $(inputs.varscans_vcf), $(inputs.muse_vcf), $(inputs.mutect_vcf), $(inputs.somsniper_vcf), $(inputs.radia_vcf), $(inputs.pindel_vcf), $(inputs.indelocator_vcf) ]
- class: InlineJavascriptRequirement
arguments:
- shellQuote: false
inputs:
varscani_vcf:
type: File
inputBinding:
prefix: -i
varscans_vcf:
type: File
inputBinding:
prefix: -i
muse_vcf:
type: File
inputBinding:
prefix: -i
mutect_vcf:
type: File
inputBinding:
prefix: -i
somsniper_vcf:
type: File
inputBinding:
prefix: -i
radia_vcf:
type: File
inputBinding:
prefix: -i
pindel_vcf:
type: File
inputBinding:
prefix: -i
indelocator_vcf:
type: File
inputBinding:
prefix: -i
tumor_analysis_uuid:
type: string?
inputBinding:
prefix: -T
tumor_bam_name:
type: string
inputBinding:
prefix: -B
tumor_aliquot_uuid:
type: string?
inputBinding:
prefix: -X
tumor_aliquot_name:
type: string
inputBinding:
prefix: -A
normal_analysis_uuid:
type: string?
inputBinding:
prefix: -n
normal_bam_name:
type: string
inputBinding:
prefix: -b
normal_aliquot_uuid:
type: string?
inputBinding:
prefix: -x
normal_aliquot_name:
type: string
inputBinding:
prefix: -a
platform:
type: string?
inputBinding:
prefix: -p
center:
type: string?
inputBinding:
prefix: -c
outputs:
reheaded_varscani:
type: File
outputBinding:
glob: varscan_indel.reheadered.vcf
reheaded_varscans:
type: File
outputBinding:
glob: varscan_fpfilter.reheadered.vcf
reheaded_muse:
type: File
outputBinding:
glob: muse_filtered.reheadered.vcf
reheaded_mutect:
type: File
outputBinding:
glob: mutect.reheadered.vcf
reheaded_radia:
type: File
outputBinding:
glob: radia_filtered.reheadered.vcf
reheaded_somsniper:
type: File
outputBinding:
glob: somatic_sniper_fpfilter.reheadered.vcf
reheaded_pindel:
type: File
outputBinding:
glob: pindel_filtered.reheadered.vcf
reheaded_indelocator:
type: File
outputBinding:
glob: indelocator_filtered.reheadered.vcf