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tomarobertstomaroberts
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Merge pull request #18 from GSTT-CSC/aide-workflows
Adds Clinical Workflow and Argo Workflow files for running on AIDE
2 parents 2eb8af3 + 277e68b commit 917b193

6 files changed

+347
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lines changed

‎app/workflows/totalsegmentator-argo-template-dgx.yaml

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metadata:
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name: totalsegmentator-argo-template
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generateName: totalsegmentator-argo-template-
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namespace: argo
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spec:
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templates:
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- name: totalsegmentator
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inputs:
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artifacts:
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- name: input-dicom
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path: /var/monai/input
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s3:
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accessKeySecret:
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name: my-minio-cred
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key: accesskey
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secretKeySecret:
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name: my-minio-cred
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key: secretkey
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key: argo/inputs/artifacts/input-dicom
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outputs:
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artifacts:
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- name: output
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path: /var/monai/output
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s3:
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bucket: bucket1
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accessKeySecret:
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name: my-minio-cred
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key: accesskey
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secretKeySecret:
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name: my-minio-cred
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key: secretkey
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key: /var/monai/output
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metadata: {}
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container:
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name: ''
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image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2
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command:
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- /bin/bash
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- '-c'
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args:
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- python3 -u /opt/monai/app/app.py
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resources:
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limits:
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cpu: '20'
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memory: 128Gi
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nvidia.com/gpu: '1'
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requests:
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cpu: '0'
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memory: '0'
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nvidia.com/gpu: '1'
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imagePullPolicy: IfNotPresent
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podSpecPatch: >-
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{"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]}
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entrypoint: totalsegmentator
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arguments: {}

‎app/workflows/totalsegmentator-argo-template-high-resource.yaml

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metadata:
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name: totalsegmentator-argo-template
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generateName: totalsegmentator-argo-template-
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namespace: argo
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spec:
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templates:
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- name: totalsegmentator
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inputs:
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artifacts:
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- name: input-dicom
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path: /var/monai/input
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s3:
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accessKeySecret:
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name: my-minio-cred
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key: accesskey
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secretKeySecret:
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name: my-minio-cred
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key: secretkey
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key: argo/inputs/artifacts/input-dicom
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outputs:
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artifacts:
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- name: output
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path: /var/monai/output
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s3:
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bucket: bucket1
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accessKeySecret:
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name: my-minio-cred
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key: accesskey
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secretKeySecret:
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name: my-minio-cred
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key: secretkey
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key: /var/monai/output
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metadata: {}
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container:
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name: ''
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image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2
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command:
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- /bin/bash
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- '-c'
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args:
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- python3 -u /opt/monai/app/app.py
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resources:
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limits:
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cpu: '8'
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memory: 64000Mi
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nvidia.com/gpu: '1'
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requests:
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cpu: '0'
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memory: '0'
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nvidia.com/gpu: '1'
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imagePullPolicy: IfNotPresent
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podSpecPatch: >-
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{"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]}
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entrypoint: totalsegmentator
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arguments: {}

‎app/workflows/totalsegmentator-argo-template-low-resource.yaml

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metadata:
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name: totalsegmentator-argo-template
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generateName: totalsegmentator-argo-template-
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namespace: argo
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spec:
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templates:
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- name: totalsegmentator
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inputs:
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artifacts:
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- name: input-dicom
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path: /var/monai/input
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s3:
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accessKeySecret:
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name: my-minio-cred
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key: accesskey
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secretKeySecret:
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name: my-minio-cred
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key: secretkey
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key: argo/inputs/artifacts/input-dicom
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outputs:
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artifacts:
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- name: output
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path: /var/monai/output
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s3:
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bucket: bucket1
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accessKeySecret:
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name: my-minio-cred
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key: accesskey
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secretKeySecret:
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name: my-minio-cred
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key: secretkey
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key: /var/monai/output
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metadata: {}
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container:
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name: ''
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image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2
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command:
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- /bin/bash
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- '-c'
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args:
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- python3 -u /opt/monai/app/app.py
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resources:
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limits:
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cpu: '1'
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memory: 8000Mi
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nvidia.com/gpu: '1'
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requests:
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cpu: '0'
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memory: '0'
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nvidia.com/gpu: '1'
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imagePullPolicy: IfNotPresent
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podSpecPatch: >-
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{"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]}
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entrypoint: totalsegmentator
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arguments: {}

‎app/workflows/totalsegmentator-argo-template-med-resource.yaml

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metadata:
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name: totalsegmentator-argo-template
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generateName: totalsegmentator-argo-template-
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namespace: argo
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spec:
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templates:
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- name: totalsegmentator
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inputs:
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artifacts:
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- name: input-dicom
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path: /var/monai/input
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s3:
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accessKeySecret:
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name: my-minio-cred
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key: accesskey
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secretKeySecret:
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name: my-minio-cred
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key: secretkey
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key: argo/inputs/artifacts/input-dicom
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outputs:
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artifacts:
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- name: output
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path: /var/monai/output
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s3:
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bucket: bucket1
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accessKeySecret:
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name: my-minio-cred
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key: accesskey
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secretKeySecret:
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name: my-minio-cred
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key: secretkey
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key: /var/monai/output
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metadata: {}
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container:
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name: ''
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image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2
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command:
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- /bin/bash
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- '-c'
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args:
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- python3 -u /opt/monai/app/app.py
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resources:
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limits:
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cpu: '4'
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memory: 16000Mi
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nvidia.com/gpu: '1'
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requests:
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cpu: '0'
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memory: '0'
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nvidia.com/gpu: '1'
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imagePullPolicy: IfNotPresent
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podSpecPatch: >-
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{"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]}
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entrypoint: totalsegmentator
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arguments: {}

‎app/workflows/totalsegmentator-argo-template.yaml

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metadata:
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name: totalsegmentator-argo-template
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generateName: totalsegmentator-argo-template-
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namespace: argo
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spec:
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templates:
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- name: totalsegmentator
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inputs:
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artifacts:
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- name: input-dicom
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path: /var/monai/input
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s3:
13+
accessKeySecret:
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name: my-minio-cred
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key: accesskey
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secretKeySecret:
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name: my-minio-cred
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key: secretkey
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key: argo/inputs/artifacts/input-dicom
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outputs:
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artifacts:
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- name: output
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path: /var/monai/output
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s3:
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bucket: bucket1
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accessKeySecret:
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name: my-minio-cred
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key: accesskey
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secretKeySecret:
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name: my-minio-cred
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key: secretkey
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key: /var/monai/output
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metadata: {}
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container:
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name: ''
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image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2
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command:
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- /bin/bash
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- '-c'
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args:
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- python3 -u /opt/monai/app/app.py
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resources:
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limits:
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cpu: '20'
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memory: 128Gi
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nvidia.com/gpu: '1'
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requests:
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cpu: '0'
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memory: '0'
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nvidia.com/gpu: '1'
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imagePullPolicy: IfNotPresent
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podSpecPatch: >-
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{"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]}
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entrypoint: totalsegmentator
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arguments: {}

‎app/workflows/totalsegmentator.json

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{
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"name": "TotalSegmentator",
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"version": "0.1.2",
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"description": "Clinical Workflow for TotalSegmentator",
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"informatics_gateway": {
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"ae_title": "MONAI",
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"data_origins": [],
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"export_destinations": [
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"PACS"
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]
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},
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"tasks": [
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{
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"id": "totalsegmentator-task",
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"description": "TotalSegmentator automatic CT segmentation",
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"type": "argo",
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"args": {
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"workflow_template_name": "totalsegmentator-argo-template",
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"server_url": "http://argo-argo-workflows-server.argo:2746",
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"namespace": "argo",
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"allow_insecure": "true"
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},
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"task_destinations": [
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{
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"name": "export-rt-struct",
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"conditions": []
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}
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],
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"export_destinations": [],
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"artifacts": {
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"input": [
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{
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"name": "input-dicom",
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"value": "{{ context.input.dicom }}",
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"mandatory": true
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}
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],
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"output": [
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{
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"name": "output",
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"value": "",
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"mandatory": true
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}
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]
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},
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"timeout_minutes": -1
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},
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{
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"id": "export-rt-struct",
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"description": "Export TotalSegmentator output RT Struct DICOMs",
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"type": "export",
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"args": {},
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"task_destinations": [],
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"export_destinations": [
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{
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"name": "PACS"
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}
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],
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"artifacts": {
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"input": [
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{
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"name": "output",
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"value": "{{ context.executions.totalsegmentator-task.artifacts.output }}",
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"mandatory": true
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}
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],
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"output": []
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},
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"timeout_minutes": -1
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}
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]
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}

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