Olamide Isreal
9e6a16c19b
Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
53 lines
1.4 KiB
YAML
53 lines
1.4 KiB
YAML
apiVersion: batch/v1
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kind: Job
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metadata:
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name: job-nextflow-digital-patient
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namespace: bioinformatics
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spec:
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backoffLimit: 1
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completionMode: NonIndexed
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completions: 1
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manualSelector: false
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parallelism: 1
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podReplacementPolicy: TerminatingOrFailed
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suspend: false
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template:
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spec:
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containers:
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- command:
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- /bin/bash
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- -c
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- cd /mnt/dreamdock-data/digital-patient-data && nextflow run test.nf -profile k8s
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image: nextflow/nextflow:25.04.6
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imagePullPolicy: IfNotPresent
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name: nextflow
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resources:
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limits:
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cpu: "4"
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memory: 8Gi
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requests:
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cpu: "2"
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memory: 4Gi
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terminationMessagePath: /dev/termination-log
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terminationMessagePolicy: File
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volumeMounts:
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- mountPath: /mnt/Avatar
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name: avatar-nas-volume
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- mountPath: /mnt/dreamdock-data/
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name: dreamdock-volume
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dnsPolicy: ClusterFirst
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restartPolicy: Never
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schedulerName: default-scheduler
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securityContext: {}
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serviceAccount: nextflow-sa
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serviceAccountName: nextflow-sa
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terminationGracePeriodSeconds: 30
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volumes:
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- name: avatar-nas-volume
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hostPath:
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path: /mnt/Avatar-NAS
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type: Directory
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- name: dreamdock-volume
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persistentVolumeClaim:
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claimName: dreamdock-data # CHANGE ME, RELATE TO nextflow.params.input
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