manifest {
    name = 'foldseek'
    author = 'Olamide'
    description = 'Nextflow pipeline for Foldseek - Fast protein structure search and clustering'
    mainScript = 'main.nf'
    version = '1.0.0'
}

params {
    query = "/omic/eureka/foldseek/input/1CRN.pdb"
    target = "/omic/eureka/foldseek/input/"
    outdir = "/omic/eureka/foldseek/output"
    mode = "search"
    sensitivity = 9.5
    evalue = 0.001
    threads = 4
    alignment_type = 2
    coverage = 0.0
    format_output = "query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits"
}

docker {
    enabled = true
}

process {
    container = 'harbor.cluster.omic.ai/omic/foldseek:latest'
    cpus = 4
    memory = '16 GB'
}

profiles {
    standard {
        docker {
            temp = 'auto'
        }
    }

    k8s {
        process {
            executor = 'k8s'
        }
        k8s {
            storageClaimName = 'eureka-pvc'
            storageMountPath = '/omic/eureka'
        }
    }
}