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validate_r1.cwl
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validate_r1.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
baseCommand: [Rscript, /usr/local/bin/validate.R]
hints:
DockerRequirement:
dockerPull: tumor_deconvolution_challenge
requirements:
- class: InlineJavascriptRequirement
inputs:
inputfile:
type: File
inputBinding:
position: 1
validation_file:
type: File
inputBinding:
position: 2
default:
class: File
location: example_files/validation_rd1.csv
json_file:
type: string
default: "results.json"
inputBinding:
position: 3
outputs:
- id: results
type: File
outputBinding:
glob: $(inputs.json_file)
- id: status
type: string
outputBinding:
glob: $(inputs.json_file)
loadContents: true
outputEval: $(JSON.parse(self[0].contents)['predictionFileStatus'])
- id: invalidReasons
type: string
outputBinding:
glob: $(inputs.json_file)
loadContents: true
outputEval: $(JSON.parse(self[0].contents)['predictionFileErrors'])