Olamide Isreal
bf04f8971e
- Update container image to harbor.cluster.omic.ai/omic/foldseek:latest - Update default paths to /omic/eureka/foldseek/ PVC mount paths - Add k8s profile with eureka-pvc storage - Remove stageInMode copy and containerOptions for k8s compatibility - Update params.json defaults to s3://omic/eureka/foldseek/ paths
49 lines
993 B
Plaintext
49 lines
993 B
Plaintext
manifest {
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name = 'foldseek'
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author = 'Olamide'
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description = 'Nextflow pipeline for Foldseek - Fast protein structure search and clustering'
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mainScript = 'main.nf'
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version = '1.0.0'
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}
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params {
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query = "/omic/eureka/foldseek/input/1CRN.pdb"
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target = "/omic/eureka/foldseek/input/"
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outdir = "/omic/eureka/foldseek/output"
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mode = "search"
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sensitivity = 9.5
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evalue = 0.001
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threads = 4
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alignment_type = 2
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coverage = 0.0
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format_output = "query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits"
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}
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docker {
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enabled = true
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}
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process {
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container = 'harbor.cluster.omic.ai/omic/foldseek:latest'
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cpus = 4
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memory = '16 GB'
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}
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profiles {
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standard {
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docker {
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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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}
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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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