nextflow.config

manifest {
    name            = 'moat'
    author          = 'Ira Cooke'
    homePage        = 'https://github.com/marine-omics/moat'
    description     = 'Marine Omics Annotation Pipeline'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.10.3'
    version = '0.1'
}


// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
 

profiles {

    test {        
        params {
            prot="${projectDir}/test/amil2_top10.prot.fa"
            cds="${projectDir}/test/amil2_top10.prot.cds.fa"
            prot2cds_map="${projectDir}/test/amil2_top10.prot2cds.map"
            split_max=5
            outdir="${launchDir}/test_out"
            max_cpus=2
            max_memory=4.GB
        }
    }

    standard {
        process.executor = 'local'
    }

    docker {
        process.executor = 'local'
        docker.enabled = true
    }

    singularity {
        process.executor = 'local'
        singularity.enabled = true
    }    

    zodiac {
        process.executor = 'pbspro'
        singularity.enabled = true
        singularity.autoMounts = true
        singularity.runOptions = '--bind /scratch/ira/ipr/interproscan-5.59-91.0/data:/opt/interproscan/data:ro'
        params.blastdb="/scratch/ira/blastdb/swissprot"
        params.pfamdb="/scratch/ira/pfam/Pfam-A.hmm"
        max_cpus=48
        max_memory=200.GB
    }


    genomics {
        process.executor = 'local'
        singularity.enabled = true
        singularity.autoMounts = true
        singularity.runOptions = '--bind /fast/shared/ipr/interproscan-5.59-91.0/data:/opt/interproscan/data:ro'
        params.blastdb="/fast/shared/blastdb/swissprot"
        params.pfamdb="/fast/shared/pfam/Pfam-A.hmm"
        max_cpus=64
        max_memory=600.GB
    }

}



// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}