9e75f44f1a
Source-only snapshot of the cluster branch for WES execution. Large reference files (HPA/MANE/ensemble FASTA, model weights, ~597 MB) are omitted: they are baked into the container images at build time and mounted from the dreamdock-data PVC at runtime, and exceed the Gitea request size limit. Pipeline entry point is main.nf, which orchestrates the biotransformer, conplex and tissue modules as a single workflow. Ligand inputs are read from the eureka workspace; protein_zarr and chembl_db come from the dreamdock-data PVC.
73 lines
1.8 KiB
YAML
73 lines
1.8 KiB
YAML
apiVersion: apps/v1
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kind: Deployment
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metadata:
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name: digital-trials-nextflow
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namespace: bioinformatics
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spec:
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progressDeadlineSeconds: 600
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replicas: 1
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revisionHistoryLimit: 10
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selector:
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matchLabels:
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app: digital-trials-nextflow
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strategy:
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rollingUpdate:
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maxSurge: 25%
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maxUnavailable: 25%
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type: RollingUpdate
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template:
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metadata:
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creationTimestamp: null
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labels:
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app: digital-trials-nextflow
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spec:
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containers:
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- command:
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- sleep
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- infinity
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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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workingDir: /mnt/dreamdock-data/digital_trials
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resources:
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limits:
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cpu: "2"
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memory: 4Gi
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requests:
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cpu: "1"
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memory: 2Gi
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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/ZINC-22
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name: zinc-22-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: Always
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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: zinc-22-volume
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hostPath:
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path: /mnt/ZINC-22
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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
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# ---
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# apiVersion: v1
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# kind: PersistentVolumeClaim
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# metadata:
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# name: digital-trials-data
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# namespace: bioinformatics
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# spec:
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# accessModes:
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# - ReadWriteMany
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# resources:
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# requests:
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# storage: 6000Gi
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# storageClassName: truenas-nfs |