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.
53 lines
1.5 KiB
YAML
53 lines
1.5 KiB
YAML
apiVersion: batch/v1
|
|
kind: Job
|
|
metadata:
|
|
name: job-nextflow-digital-trials
|
|
namespace: bioinformatics
|
|
spec:
|
|
backoffLimit: 1
|
|
completionMode: NonIndexed
|
|
completions: 1
|
|
manualSelector: false
|
|
parallelism: 1
|
|
podReplacementPolicy: TerminatingOrFailed
|
|
suspend: false
|
|
template:
|
|
spec:
|
|
containers:
|
|
- command:
|
|
- /bin/bash
|
|
- -c
|
|
- cd /mnt/dreamdock-data/digital_trials && nextflow run main.nf -profile k8s ## CHANGE ME
|
|
image: nextflow/nextflow:25.04.6
|
|
imagePullPolicy: IfNotPresent
|
|
name: nextflow
|
|
resources:
|
|
limits:
|
|
cpu: "4"
|
|
memory: 8Gi
|
|
requests:
|
|
cpu: "2"
|
|
memory: 4Gi
|
|
terminationMessagePath: /dev/termination-log
|
|
terminationMessagePolicy: File
|
|
volumeMounts: ## CHANGE ME
|
|
- mountPath: /mnt/ZINC-22
|
|
name: zinc-22-volume
|
|
- mountPath: /mnt/dreamdock-data
|
|
name: dreamdock-volume
|
|
dnsPolicy: ClusterFirst
|
|
restartPolicy: Never
|
|
schedulerName: default-scheduler
|
|
securityContext: {}
|
|
serviceAccount: nextflow-sa
|
|
serviceAccountName: nextflow-sa
|
|
terminationGracePeriodSeconds: 30
|
|
volumes: ## CHANGE ME
|
|
- name: zinc-22-volume
|
|
hostPath:
|
|
path: /mnt/ZINC-22
|
|
type: Directory
|
|
- name: dreamdock-volume
|
|
persistentVolumeClaim:
|
|
claimName: dreamdock-data
|