kraken-nf/nextflow.config at master · maxibor/kraken-nf · GitHub

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process.container = "maxibor/kraken_nf:latest"

params {
    reads = ''
    minimum_read_length = 35
    krakendb = '/path/to/minikraken2_v2_8GB_201904_UPDATE.tgz'
    kraken_mem = '9G'
    phred = 33
    results = './results'
    collapse = false
    minhit = 10
    pairedEnd = true
    help = false
    kraken_kmer_len = 35
    build_bracken_db = false
    run_bracken = true
    bracken_level = "S"
    bracken_threshold = "10"

}

profiles {
    docker {
        docker.enabled = true
        docker.runOptions = '-u \$(id -u):\$(id -g)'
    }
    singularity {
        singularity.enabled = true
        singularity.autoMounts = true
    }
    conda {
        process {
            conda = "$baseDir/envs/environment.yml"
        }
    }
    standard {
        executor {
            name = 'local'
        }
         process{
            withLabel : 'intenso' {
                cpus = 8
                memory = params.kraken_mem
            }
            withLabel : 'expresso' {
                cpus = 6
                memory = '2G'
            }
            withLabel : 'ristretto' {
                cpus = 1
                memory = '2G'
            }
        }
    }
    test {
        params {
            reads = "$baseDir/test/reads/*.{1,2}.trimmed.fastq.gz"
            krakendb = "$baseDir/test/kraken/simple"
            phred = 33
            minhit = 2
            collapse = true
        }
        executor {
            name = 'local'
        }
         process{
            cpus = 1
            memory = '1G'
        }
    }
    eva {
        executor {
            queueSize = 8
        }
        process{
            executor = 'sge'
            penv = 'smp'
            queue = 'archgen.q'
            clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }

            withLabel : 'intenso' {
                cpus = 8
                memory = params.kraken_mem
            }
            withLabel : 'expresso' {
                cpus = 6
                memory = '4G'
            }
            withLabel : 'ristretto' {
                cpus = 1
                memory = '4G'
            }
        }
    }
}