Olamide Isreal
b099a5ee38
Add standard, k8s, and k8s_gpu profiles matching reference tool patterns. Configure PVC mounting for eureka storage and GPU node selection. Remove Docker-specific containerOptions from process definition.
81 lines
1.9 KiB
Plaintext
81 lines
1.9 KiB
Plaintext
// Manifest for Nextflow metadata
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manifest {
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name = 'RoseTTAFold-All-Atom'
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author = 'Baker Laboratory'
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homePage = 'https://github.com/baker-laboratory/RoseTTAFold-All-Atom'
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description = 'Nextflow pipeline for RoseTTAFold-All-Atom biomolecular structure prediction'
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mainScript = 'main.nf'
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version = '1.0.0'
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}
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// Global default parameters
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params {
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// Input files
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protein_fasta = "s3://omic/eureka/rosettafold-all-atom/input/protein.fasta"
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na_fasta = ""
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na_type = "dna"
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sm_file = ""
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sm_type = "sdf"
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covale_inputs = ""
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// Output
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outdir = "s3://omic/eureka/rosettafold-all-atom/output"
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job_name = "rfaa_prediction"
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// Model settings
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max_cycle = 4
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// Database paths
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db_uniref30 = "/mnt/databases/UniRef30_2020_06"
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db_bfd = "/mnt/databases/bfd"
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db_pdb100 = "/mnt/databases/pdb100_2021Mar03"
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weights = "/mnt/databases/RFAA_paper_weights.pt"
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}
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// Profiles
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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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runOptions = '--gpus all -v /mnt:/mnt'
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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/rosettafold-all-atom: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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k8s_gpu {
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process {
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executor = 'k8s'
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container = 'harbor.cluster.omic.ai/omic/rosettafold-all-atom:latest'
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pod = [[nodeSelector: 'nvidia.com/gpu.present=true']]
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accelerator = [request: 1, type: 'nvidia.com/gpu']
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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 = 8
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memory = '64 GB'
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}
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