workflow.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow
label: <YOUR CHALLENGE> Evaluation
doc: >
  BRIEF DESCRIPTION ABOUT THE CHALLENGE, e.g.
  This workflow will run and evaluate Docker submissions to the
  Awesome Challenge (syn123). Metrics returned are x, y, z.

requirements:
  - class: StepInputExpressionRequirement

inputs:
  submissionId:
    label: Submission ID
    type: int
  submitterUploadSynId:
    label: Synapse Folder ID accessible by the submitter
    type: string
  synapseConfig:
    label: filepath to .synapseConfig file
    type: File

outputs: {}

steps:

  set_submitter_folder_permissions:
    run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/set_permissions.cwl
    in:
      - id: entityid
        source: "#submitterUploadSynId"
      - id: principalid
        valueFrom: "3477032"
      - id: permissions
        valueFrom: "download"
      - id: synapse_config
        source: "#synapseConfig"
    out: []

  download_submission:
    run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/get_submission.cwl
    in:
      - id: submissionid
        source: "#submissionId"
      - id: synapse_config
        source: "#synapseConfig"
    out:
      - id: filepath
      - id: docker_repository
      - id: docker_digest
      - id: entity_id
      - id: evaluation_id
      - id: entity_type
      - id: results
      
  download_goldstandard:
    run: https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/cwl-tool-synapseclient/v1.4/cwl/synapse-get-tool.cwl
    in:
      # TODO: replace `valueFrom` with the Synapse ID to the challenge goldstandard
      - id: synapseid
        valueFrom: "syn53645141"
      - id: synapse_config
        source: "#synapseConfig"
    out:
      - id: filepath

  validate:
    run: steps/validate.cwl
    in:
      - id: evaluation_id
        source: "#download_submission/evaluation_id"
      - id: input_file
        source: "#download_submission/filepath"
      - id: validate_script
        default:
          class: File
          location: "scripts/validate.py"
    out:
      - id: results
      - id: status
      - id: invalid_reasons
  
  email_validation:
    run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/validate_email.cwl
    in:
      - id: submissionid
        source: "#submissionId"
      - id: synapse_config
        source: "#synapseConfig"
      - id: status
        source: "#validate/status"
      - id: invalid_reasons
        source: "#validate/invalid_reasons"
      # OPTIONAL: set `default` to `false` if email notification about valid submission is needed
      - id: errors_only
        default: true
    out: [finished]

  annotate_validation_with_output:
    run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/annotate_submission.cwl
    in:
      - id: submissionid
        source: "#submissionId"
      - id: annotation_values
        source: "#validate/results"
      - id: to_public
        default: true
      - id: force
        default: true
      - id: synapse_config
        source: "#synapseConfig"
    out: [finished]

  check_status:
    run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/check_status.cwl
    in:
      - id: status
        source: "#validate/status"
      - id: previous_annotation_finished
        source: "#annotate_validation_with_output/finished"
      - id: previous_email_finished
        source: "#email_validation/finished"
    out: [finished]

  score:
    run: steps/score.cwl
    in:
      - id: evaluation_id
        source: "#download_submission/evaluation_id"
      - id: input_file
        source: "#download_submission/filepath"
      - id: groundtruth_path
        source: "#download_goldstandard/filepath"
        # valueFrom: "/home/ec2-user/challenge-data/TestingData"
        # valueFrom: "/Users/rchai/DREAM/Dynamic-AI/Data/TestingData"
      - id: score_script
        default:
          class: File
          location: "scripts/score.py"
    out:
      - id: results
      - id: status

  email_score:
    run: steps/email_scores.cwl
    in:
      - id: submissionid
        source: "#submissionId"
      - id: synapse_config
        source: "#synapseConfig"
      - id: results
        source: "#score/results"
      # OPTIONAL: add annotations to be withheld from participants to `[]`
      # - id: private_annotations
      #   default: []
    out: [finished]

  annotate_submission_with_output:
    run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/annotate_submission.cwl
    in:
      - id: submissionid
        source: "#submissionId"
      - id: annotation_values
        source: "#score/results"
      - id: to_public
        default: true
      - id: force
        default: true
      - id: synapse_config
        source: "#synapseConfig"
      - id: previous_annotation_finished
        source: "#annotate_validation_with_output/finished"
    out: [finished]
 
  check_score_status:
    run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/check_status.cwl
    in:
      - id: status
        source: "#score/status"
      - id: previous_annotation_finished
        source: "#annotate_submission_with_output/finished"
      - id: previous_email_finished
        source: "#email_score/finished"
    out: [finished]