// Manifest for Nextflow metadata
manifest {
    name = 'PROPKA-Nextflow'
    author = 'Olamide'
    homePage = 'https://github.com/jensengroup/propka'
    description = 'Nextflow pipeline for PROPKA - Empirical pKa prediction for proteins and protein-ligand complexes'
    mainScript = 'main.nf'
    version = '1.0.0'
}

// Global default parameters
params {
    pdb = null
    outdir = null
    ph = 7.0
    options = ""
}

profiles {
    standard {
        docker {
            enabled = true
            runOptions = '--rm'
        }
    }
    k8s {
        process {
            executor = 'k8s'
        }
        docker {
            enabled = true
        }
        k8s {
            storageClaimName = 'eureka-pvc'
            storageMountPath = '/omic/eureka'
        }
    }
}

// Process configurations
process {
    cpus = 1
    memory = '4 GB'
}