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prefect.yaml
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# Welcome to your prefect.yaml file! You can use this file for storing and managing
# configuration for deploying your flows. We recommend committing this file to source
# control along with your flow code.
# Generic metadata about this project
name: s3-Prefect-Workflow
prefect-version: 2.14.19
# build section allows you to manage and build docker images
build: null
# push section allows you to manage if and how this project is uploaded to remote locations
push: null
# pull section allows you to provide instructions for cloning this project in remote locations
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: main
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# the deployments section allows you to provide configuration for deploying flows
deployments:
# base metadata
- name: ccdi-data-curation-2gb
version: null
tags: ["Production"]
description: null
entrypoint: workflows/s3-Prefect-Pipeline.py:runner
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
file_path: "inputs/CCDI_Submission_Template_v1.9.1_20Exampler.xlsx"
#runner: "your_uniq_id"
#optional parmaeters below, uncomment if needed
#output_folder: "output_folder_name"
#template_path: "inputs/CCDI_Submission_Template_v1.7.1.xlsx"
#sra_template_path: "inputs/phsXXXXXX.xlsx"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.3.2
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-2gb
work_queue_name: null
job_variables: {}
- name: ccdi-data-curation-8gb
version: null
tags: ["Production"]
description: null
entrypoint: workflows/s3-Prefect-Pipeline.py:runner
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
file_path: "inputs/CCDI_Submission_Template_v1.9.1_20Exampler.xlsx"
#runner: "your_uniq_id"
#optional parmaeters below, uncomment if needed
#output_folder: "output_folder_name"
#template_path: "inputs/CCDI_Submission_Template_v1.7.1.xlsx"
#sra_template_path: "inputs/phsXXXXXX.xlsx"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.3.2
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-8gb
work_queue_name: null
job_variables: {}
- name: ccdi-data-curation-16gb
version: null
tags: ["Production"]
description: null
entrypoint: workflows/s3-Prefect-Pipeline.py:runner
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
file_path: "inputs/CCDI_Submission_Template_v1.9.1_20Exampler.xlsx"
#runner: "your_uniq_id"
#optional parmaeters below, uncomment if needed
#output_folder: "output_folder_name"
#template_path: "inputs/CCDI_Submission_Template_v1.7.1.xlsx"
#sra_template_path: "inputs/phsXXXXXX.xlsx"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.3.2
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-16gb
work_queue_name: null
job_variables: {}
- name: ccdi-data-curation-32gb
version: null
tags: ["Production"]
description: null
entrypoint: workflows/s3-Prefect-Pipeline.py:runner
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
file_path: "inputs/CCDI_Submission_Template_v1.9.1_20Exampler.xlsx"
#runner: "your_uniq_id"
#optional parmaeters below, uncomment if needed
#output_folder: "output_folder_name"
#template_path: "inputs/CCDI_Submission_Template_v1.7.1.xlsx"
#sra_template_path: "inputs/phsXXXXXX.xlsx"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.3.2
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-32gb
work_queue_name: null
job_variables: {}
- name: ccdi-data-curation-60gb
version: null
tags: ["Production"]
description: null
entrypoint: workflows/s3-Prefect-Pipeline.py:runner
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
file_path: "inputs/CCDI_Submission_Template_v1.9.1_20Exampler.xlsx"
#runner: "your_uniq_id"
#optional parmaeters below, uncomment if needed
#output_folder: "output_folder_name"
#template_path: "inputs/CCDI_Submission_Template_v1.7.1.xlsx"
#sra_template_path: "inputs/phsXXXXXX.xlsx"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.3.2
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-60gb
work_queue_name: null
job_variables: {}
- name: bucket-reader-2gb
version: null
tags: ["Production"]
description: null
entrypoint: workflows/bucket_reader.py:reader
schedule: null
# flow-specific parameters
parameters:
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.1
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-2gb
work_queue_name: null
job_variables: {}
- name: template-exampler
version: null
tags: ["Production"]
description: null
entrypoint: workflows/Template_Exampler.py:run_template_exampler
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
number_of_entries: 20
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.1
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-2gb
work_queue_name: null
job_variables: {}
- name: ccdi-file-copier
version: null
tags: ["Production"]
description: null
entrypoint: workflows/File_Mover.py:file_mover
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: main
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-60gb
work_queue_name: null
job_variables: {}
- name: get-parameter-2gb
version: null
tags: ["Test"]
description: null
entrypoint: workflows/get_aws_parameter.py:get_aws_parameter
schedule: null
# flow-specific parameters
parameters:
parameter_name: "prefect-test"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: main
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-2gb
work_queue_name: null
job_variables: {}
- name: pull-neo4j-data-8gb-ccdi
version: null
tags: ["Production"]
description: null
entrypoint: workflows/pull_neo4j_data.py:pull_neo4j_data
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
uri_parameter: "uri"
username_parameter: "username"
password_parameter: "password"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: main
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-8gb
work_queue_name: null
job_variables: {}
- name: pull-neo4j-data-16gb-c3dc
version: null
tags: ["Production"]
description: null
entrypoint: workflows/pull_neo4j_data.py:pull_neo4j_data
schedule: null
# flow-specific parameters
parameters:
bucket: "c3dc-curation"
uri_parameter: "uri"
username_parameter: "username"
password_parameter: "password"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: main
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-c3dc-16gb
work_queue_name: null
job_variables: {}
- name: validate-neo4j-data-32gb
version: null
tags: ["Production"]
description: null
entrypoint: workflows/validate_neo4j_data.py:validate_neo4j_data
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.1
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-32gb
work_queue_name: null
job_variables: {}
- name: ccdi-guid-checker-32gb
version: null
tags: ["Production"]
description: null
entrypoint: workflows/guid_checker.py:guid_checker_runner
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
file_path: "inputs/CCDI_Submission_Template_v1.7.2_10ExampleR20231228.xlsx"
runner: "your_uniq_id"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: main
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-32gb
work_queue_name: null
job_variables: {}
# base metadata
- name: model-mapping-maker-8gb
version: null
tags: ["Production"]
description: null
entrypoint: workflows/model_mapping_maker.py:runner
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
runner: "your_uniq_id"
old_model_repository: "ccdi-model"
new_model_repository: "ccdi-model"
old_model_file_location: "model-desc/ccdi-model.yml"
new_model_file_location: "model-desc/ccdi-model.yml"
old_model_version: ""
new_model_version: ""
base_mode: False
nodes_mapping_file: "path_to/nodes_file/in/s3_bucket"
relationship_mapping_file: "path_to/nodes_file/in/s3_bucket"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.1
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-8gb
work_queue_name: null
job_variables: {}
- name: ccdi-template-liftover
version: null
tags: ["Production"]
description: null
entrypoint: workflows/ccdi_manifest_liftover.py:manifest_liftover
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
lift_to_tag: "1.9.1"
liftover_mapping_filepath: "Model_Mapping_Maker/1.7.2-1.9.1/model_mapping_maker_20240718_T133843/1.7.2_1.9.1_MAPPING_20240718.tsv"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.1
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-32gb
work_queue_name: null
job_variables: {}
- name: dcf-index
version: null
tags: ["Production"]
description: null
entrypoint: workflows/dcf_indexing.py:dcf_index_manifest
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.1
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-8gb
work_queue_name: null
job_variables: {}
- name: fetch-size-md5sum
version: null
tags: ["Production"]
description: null
entrypoint: workflows/fetch_size_md5sum.py:get_size_md5sum
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.1
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-8gb
work_queue_name: null
job_variables: {}
- name: file-remover
version: null
tags: ["Production"]
description: null
entrypoint: workflows/File_Remover.py:run_file_remover
schedule: null
# flow-specific parameters
parameters:
# pull action to overwrite from file pull action
pull:
- prefect.deployments.steps.git_clone:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.1.1
- prefect.deployments.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-32gb
work_queue_name: null
job_variables: {}
- name: get-parameter
version: null
tags: ["Production"]
description: null
entrypoint: workflows/get_aws_parameter.py:get_aws_parameter
schedule: null
# flow-specific parameters
parameters:
parameter_name: "prefect-test"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.1
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-2gb
work_queue_name: null
job_variables: {}
- name: join-tsv-to-manifest
version: null
tags: ["Production"]
description: null
entrypoint: workflows/db_tsv_to_manifest.py:join_tsv_to_manifest
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.16
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-16gb
work_queue_name: null
job_variables: {}
- name: mci-release-manifest
version: null
tags: ["Production"]
description: null
entrypoint: workflows/mci_release_run.py:mci_release_manifest
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
template_tag: "2.1.0"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.3.3
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-8gb
work_queue_name: null
job_variables: {}
- name: model-to-submission
version: null
tags: ["Production"]
description: null
entrypoint: workflows/model_to_submission.py:create_submission_manifest
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.1
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-2gb
work_queue_name: null
job_variables: {}
- name: new-model-validation
version: null
tags: ["Production"]
description: null
entrypoint: workflows/new_model_validation.py:validate_new_model
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.1
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-2gb
work_queue_name: null
job_variables: {}
- name: submission-cruncher
version: null
tags: ["Production"]
description: null
entrypoint: workflows/Submission_Cruncher.py:submission_cruncher
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.1
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-8gb
work_queue_name: null
job_variables: {}
- name: file-mover
version: null
tags: ["Production"]
description: null
entrypoint: workflows/file_mover_delete.py:file_mover_delete
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.3
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-32gb
work_queue_name: null
job_variables: {}
- name: ccdi-to-sra
version: null
tags: ["TEST"]
description: null
entrypoint: workflows/ccdi_to_sra.py:run_ccdi_to_sra
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: CCDIDC-1334_sra_library_id
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-60gb
work_queue_name: null
job_variables: {}
- name: neo4j-stats
version: null
tags: ["Production"]
description: null
entrypoint: workflows/neo4j_stats.py:pull_neo4j_stats
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: main
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-32gb
work_queue_name: null
job_variables: {}
- name: join-tsv-to-manifest_OLD
version: null
tags: ["Production"]
description: null
entrypoint: workflows/db_tsv_to_manifest.py:join_tsv_to_manifest
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.0.1
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
- name: guid-meta-check
version: null
tags: ["Production"]
description: null
entrypoint: src/sandbox_indexd_guid_validation.py:guid_validation_between_sandbox_indexd
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.1.7
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
- name: DB-props-uniq-report
version: null
tags: ["Production"]
description: null
entrypoint: src/neo4j_data_tools.py:report_unique_values_properties
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.2.0
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-8gb
work_queue_name: null
job_variables: {}
- name: bucket-content-search
version: null
tags: ["Production"]
description: null
entrypoint: src/search_bucket_content.py:search_buckets_content
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: 1.2.2
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-8gb
work_queue_name: null
job_variables: {}
- name: ccdi-gdc-transformation-16gb
version: null
tags: ["Production"]
description: null
entrypoint: workflows/ccdi_to_gdc.py:ccdi_to_gdc_run
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
runner: "runner_id"
file_path: "inputs/CCDI_Submission_Template_v1.9.1_20Exampler.xlsx"
ccdi_gdc_translation_file: ""
platform_preservation_file: ""
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: CCDIDC-1640-Fix-CCDI-output-to-GDC
- prefect.projects.steps.pip_install_requirements:
requirements_file: requirements.txt
directory: "{{ clone-step.directory }}"
stream_output: False
# infra-specific fields
work_pool:
name: ccdi-curation-16gb
work_queue_name: null
job_variables: {}
# base metadata
- name: ccdi-gdc-import
version: null
tags: ["Production"]
description: null
entrypoint: workflows/gdc_import.py:runner
schedule: null
# flow-specific parameters
parameters:
bucket: "ccdi-validation"
file_path: ""
runner: ""
node_type: "case"
secret_name_path: "ccdi/nonprod/inventory/gdc-token"
secret_key_name: "gdc-token"
project_id: "CCDI-MCI"
sstr: "phs002790.v7"
check_for_updates: "yes"
# pull action to overwrite from file pull action
pull:
- prefect.projects.steps.git_clone_project:
id: clone-step
repository: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline.git
branch: main