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task2_workflow.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: RARE-X A Rare Disease Open Science Data Challenge Evaluation Task 2
doc: >
This workflow will run and evaluate Docker submissions to the
RARE-X Challenge (syn51198355). A single metric will be returned:
accuracy.
requirements:
- class: StepInputExpressionRequirement
inputs:
adminUploadSynId:
label: Synapse Folder ID accessible by an admin
type: string
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
workflowSynapseId:
label: Synapse File ID that links to the workflow
type: string
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"
# TODO: replace `valueFrom` with the admin user ID or admin team ID
- id: principalid
valueFrom: "3468096"
- id: permissions
valueFrom: "download"
- id: synapse_config
source: "#synapseConfig"
out: []
set_admin_folder_permissions:
run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/set_permissions.cwl
in:
- id: entityid
source: "#adminUploadSynId"
# TODO: replace `valueFrom` with the admin user ID or admin team ID
- id: principalid
valueFrom: "3468096"
- id: permissions
valueFrom: "download"
- id: synapse_config
source: "#synapseConfig"
out: []
get_docker_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: entity_type
- id: results
get_docker_config:
run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/get_docker_config.cwl
in:
- id: synapse_config
source: "#synapseConfig"
out:
- id: docker_registry
- id: docker_authentication
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: "syn51704122"
- id: synapse_config
source: "#synapseConfig"
out:
- id: filepath
validate_docker:
run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/validate_docker.cwl
in:
- id: submissionid
source: "#submissionId"
- id: synapse_config
source: "#synapseConfig"
out:
- id: results
- id: status
- id: invalid_reasons
email_docker_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_docker/status"
- id: invalid_reasons
source: "#validate_docker/invalid_reasons"
# OPTIONAL: set `default` to `false` if email notification about valid submission is needed
- id: errors_only
default: true
out: [finished]
annotate_docker_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_docker/results"
- id: to_public
default: true
- id: force
default: true
- id: synapse_config
source: "#synapseConfig"
out: [finished]
check_docker_status:
run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/check_status.cwl
in:
- id: status
source: "#validate_docker/status"
- id: previous_annotation_finished
source: "#annotate_docker_validation_with_output/finished"
- id: previous_email_finished
source: "#email_docker_validation/finished"
out: [finished]
run_docker:
run: steps/run_docker.cwl
in:
- id: docker_repository
source: "#get_docker_submission/docker_repository"
- id: docker_digest
source: "#get_docker_submission/docker_digest"
- id: submissionid
source: "#submissionId"
- id: docker_registry
source: "#get_docker_config/docker_registry"
- id: docker_authentication
source: "#get_docker_config/docker_authentication"
- id: status
source: "#validate_docker/status"
- id: parentid
source: "#submitterUploadSynId"
- id: synapse_config
source: "#synapseConfig"
# OPTIONAL: set `default` to `false` if log file should not be uploaded to Synapse
- id: store
default: false
# TODO: replace `valueFrom` with the absolute path to the data directory to be mounted
- id: input_dir
valueFrom: "/home/ec2-user/grnd_trth" #add filepath where the data is mounted from in the instance add folder for task2 data via commandline
- id: docker_script
default:
class: File
location: "scripts/run_docker.py"
out:
- id: predictions
upload_results:
run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/upload_to_synapse.cwl
in:
- id: infile
source: "#run_docker/predictions"
- id: parentid
source: "#adminUploadSynId"
- id: used_entity
source: "#get_docker_submission/entity_id"
- id: executed_entity
source: "#workflowSynapseId"
- id: synapse_config
source: "#synapseConfig"
out:
- id: uploaded_fileid
- id: uploaded_file_version
- id: results
annotate_docker_upload_results:
run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/annotate_submission.cwl
in:
- id: submissionid
source: "#submissionId"
- id: annotation_values
source: "#upload_results/results"
- id: to_public
default: true
- id: force
default: true
- id: synapse_config
source: "#synapseConfig"
- id: previous_annotation_finished
source: "#annotate_docker_validation_with_output/finished"
out: [finished]
validate:
run: steps/validate.cwl
in:
- id: input_file
source: "#run_docker/predictions"
- id: goldstandard
source: "#download_goldstandard/filepath"
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"
- id: previous_annotation_finished
source: "#annotate_docker_upload_results/finished"
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: predictions_file
source: "#run_docker/predictions"
- id: goldstandard
source: "#download_goldstandard/filepath"
- id: check_validation_finished
source: "#check_status/finished"
out:
- id: results
email_score:
run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/score_email.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: []
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]