// Manifest for Nextflow metadata
manifest {
    name = 'Foldseek-Nextflow'
    author = 'Generated from Foldseek repository'
    homePage = 'https://github.com/steineggerlab/foldseek'
    description = 'Nextflow pipeline for Foldseek - Fast protein structure search and clustering'
    mainScript = 'main.nf'
    version = '1.0.0'
}

// Global default parameters
params {
    query = "/mnt/OmicNAS/private/old/olamide/foldseek/input/1CRN.pdb"
    target = "/mnt/OmicNAS/private/old/olamide/foldseek/input/"
    outdir = "/mnt/OmicNAS/private/old/olamide/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"
}

// Container configurations
docker {
    enabled = true
    runOptions = '-v /mnt:/mnt'
}

// Process configurations
process {
    cpus = 4
    memory = '16 GB'
}

// Execution configurations
executor {
    $local {
        cpus = 8
        memory = '32 GB'
    }
}