Olamide Isreal
35dd4ab976
PVC mount is not available in k8s pods. Try multiple fallback methods to retrieve input PDB: PVC path, s3-to-PVC conversion, AWS CLI from MinIO, and curl from MinIO. Also add nf-amazon plugin and s3:// default paths.
59 lines
1.2 KiB
Plaintext
59 lines
1.2 KiB
Plaintext
// Manifest for Nextflow metadata
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manifest {
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name = 'pocketminer-Nextflow'
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author = 'Olamide'
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homePage = 'https://github.com/Mickdub/gvp'
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description = 'Nextflow pipeline for PocketMiner - cryptic binding pocket prediction using geometric deep learning'
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mainScript = 'main.nf'
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version = '1.0.0'
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}
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// S3/MinIO plugin for direct S3 access (bypasses PVC mount issues)
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plugins {
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id 'nf-amazon'
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}
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aws {
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client {
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endpoint = 'http://datalake-hl.datalake.svc.cluster.local:9000'
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s3PathStyleAccess = true
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}
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}
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// Global default parameters
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params {
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pdb = "s3://omic/eureka/Pocketminer/1HSG.pdb"
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outdir = "s3://omic/eureka/Pocketminer/output"
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debug = false
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}
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// Profiles for different execution environments
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profiles {
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standard {
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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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}
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k8s {
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process {
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executor = 'k8s'
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container = 'harbor.cluster.omic.ai/omic/pocketminer:latest'
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}
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docker {
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enabled = true
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}
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k8s {
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storageClaimName = 'eureka-pvc'
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storageMountPath = '/omic/eureka'
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}
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}
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}
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// Process configurations
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process {
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cpus = 2
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memory = '8 GB'
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}
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