Olamide Isreal
9e6a16c19b
Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
99 lines
2.2 KiB
Plaintext
99 lines
2.2 KiB
Plaintext
manifest {
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name = 'digital patients'
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author = 'omic'
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recurseSubmodules = true
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homePage = 'https://gitlab.com/omic/next/registry/pipelines/digitalpatients'
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description = 'generative digital patients and multi-omics pipeline'
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mainScript = 'main.nf'
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nextflowVersion = '!>=21.04.3'
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defaultBranch = 'master'
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}
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// docker {
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// enabled = true
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// temp = 'auto'
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// }
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// process {
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// withLabel: 'gpu_process' {
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// containerOptions = '--gpus all --rm'
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// }
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//
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// withLabel: 'cpu_process' {
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// containerOptions = '--rm'
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// }
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// }
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def sharedPod = [
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[env: 'NXF_DEBUG', value: '0'],
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[label: 'omic-app', value: 'digitalpatients'],
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[imagePullSecret: 'gitlab-registry-secret'],
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[volumeClaim: 'avatar-new', mountPath: '/mnt/Avatar/'],
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]
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profiles {
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docker {
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docker.enabled = true
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process {
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executor = 'local'
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withLabel: 'gpu_process' {
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maxForks = 1 // Only one GPU task at a time on single GPU system
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containerOptions = '--gpus all --rm'
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}
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withLabel: 'cpu_process' {
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containerOptions = '--rm'
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}
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}
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}
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k8s {
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process {
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executor = 'k8s'
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namespace = 'bioinformatics'
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debug = true
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pod = sharedPod
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withLabel: 'gpu_process' {
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pod = sharedPod + [
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[nodeSelector: [gpu: 'yes', 'gpu-type': 'geforce-rtx-3090']]
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]
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}
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}
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workDir = "/mnt/dreamdock-data/digital-patient-data/work"
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k8s {
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serviceAccount = 'nextflow-sa'
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namespace = 'bioinformatics'
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storageClaimName = 'dreamdock-data'
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storageMountPath = '/mnt/dreamdock-data'
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pullPolicy = 'IfNotPresent'
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cleanup = true // delete pods after Ctrl+C or finished?
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// cleanup = false // delete pods after Ctrl+C or finished?
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// RUN AS DIFFERENT USERS
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// securityContext = [fsGroup: 1000]
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// securityContext = [
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// runAsUser: 1000,
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// fsGroup: 1000,
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// runAsNonRoot: true
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// ]
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}
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// Use container image
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// process.container = 'harbor.cluster.omic.ai/omic/faiss-indexer:latest'
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}
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}
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