template.yaml

workflow:
    version: 0.3.0
    inputs:
      files:
        - $[[code]]
        - code/analyze.py
        - data/sequences.txt
        - data/gt.txt
      parameters:
        codefile: code/predict.py
        inputfile: data/sequences.txt
        gtfile: data/gt.txt
        outputfile: results/predict.txt
    workflow:
      type: serial
      specification:
        steps:
          - environment: $[[environ]]
            commands:
              - $[[command]]
              - python code/analyze.py
                  --resultfile "${outputfile}"
                  --gtfile "${gtfile}"
                  --outputfile results/analytics.json
    outputs:
      files:
       - results/predict.txt
       - results/analytics.json
parameters:
    - id: 'code'
      name: 'Code file'
      datatype: 'file'
      defaultValue: 'code/predict.py'
      as: '$input'
      index: 2
    - id: 'environ'
      name: 'Environment'
      datatype: 'string'
      defaultValue: 'python:3.7'
      index: 0
    - id: 'command'
      name: 'Command'
      datatype: 'string'
      defaultValue: 'python code/predict.py -i "${inputfile}" -o "${outputfile}"'
      index: 1
results:
    file: results/analytics.json
    schema:
        - id: avg_diff
          name: 'Deviation'
          type: decimal
        - id: exact_match
          name: 'Exact Predictions'
          type: int
    orderBy:
        - id: avg_diff
          sortDesc: false
        - id: exact_match
          sortDesc: true