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.
114 lines
2.6 KiB
Plaintext
114 lines
2.6 KiB
Plaintext
// Nextflow configuration file
|
|
|
|
// Execution report
|
|
report {
|
|
enabled = true
|
|
file = "execution_report.html"
|
|
overwrite = true}
|
|
|
|
|
|
// Resource usage tracking
|
|
trace {
|
|
enabled = true
|
|
file = "execution_trace.txt"
|
|
overwrite = true
|
|
}
|
|
|
|
// Error reporting
|
|
timeline {
|
|
enabled = true
|
|
file = "execution_timeline.html"
|
|
overwrite = true
|
|
}
|
|
|
|
// // Max resources
|
|
// executor {
|
|
// $local {
|
|
// memory = '80 GB'
|
|
// cpus = 2
|
|
// }
|
|
// }
|
|
|
|
// Default parameters (overridden by test.nf)
|
|
params {
|
|
// Set defaults here
|
|
// input = '/mnt/ZINC-22/conplex/total.zarr'
|
|
nshards = 12
|
|
outdir = "$launchDir"
|
|
}
|
|
|
|
profiles {
|
|
k8s {
|
|
process.executor = 'k8s'
|
|
process.namespace = 'bioinformatics'
|
|
process.debug = true
|
|
|
|
workDir = "/workdir/work"
|
|
|
|
k8s {
|
|
serviceAccount = 'nextflow-sa'
|
|
namespace = 'bioinformatics'
|
|
storageClaimName = 'conplex-data'
|
|
storageMountPath = '/workdir'
|
|
|
|
pullPolicy = 'IfNotPresent'
|
|
cleanup = true // delete pods after Ctrl+C or finished?
|
|
|
|
|
|
// RUN AS DIFFERENT USERS
|
|
// securityContext = [fsGroup: 1000]
|
|
// securityContext = [
|
|
// runAsUser: 1000,
|
|
// fsGroup: 1000,
|
|
// runAsNonRoot: true
|
|
// ]
|
|
}
|
|
|
|
// Use container image
|
|
// process.container = 'harbor.cluster.omic.ai/omic/faiss-indexer:latest'
|
|
|
|
// Pod-level customization
|
|
process.pod = [
|
|
[env: 'NXF_DEBUG', value: '0'],
|
|
[label: 'omic-app', value: 'conplex'],
|
|
[imagePullSecret: 'gitlab-registry-secret'],
|
|
[volumeClaim: 'fingerprint-data', mountPath: '/fingerprint-data']
|
|
//[nodeSelector: [gpu: 'yes', 'kubernetes.io/hostname': 'k8s-node25']],
|
|
// [privileged: true],
|
|
]
|
|
|
|
// process {
|
|
// withName: 'trainIndex' {
|
|
// container = 'harbor.cluster.omic.ai/omic/conplex-faiss-train:latest'
|
|
// accelerator = 1
|
|
// memory = '75 GB'
|
|
// cpus = 1
|
|
|
|
// // GPU-specific pod settings
|
|
// pod = [
|
|
// [nodeSelector: [gpu: 'yes']]
|
|
// ]
|
|
// }
|
|
|
|
// // Specific settings for addToIndex process (CPU only)
|
|
// withName: 'addToIndex' {
|
|
// container = 'harbor.cluster.omic.ai/omic/conplex-faiss-add:latest'
|
|
// memory = '75 GB'
|
|
// cpus = 1
|
|
|
|
// // Explicitly ensure no GPU requirements
|
|
// // No accelerator property set, and no GPU nodeSelector
|
|
// }
|
|
// }
|
|
}
|
|
|
|
docker {
|
|
// Docker/Singularity configuration
|
|
docker {
|
|
enabled = true
|
|
runOptions = '--rm'
|
|
}
|
|
}
|
|
}
|
|
|