nextflow.config

/*
 * Pipeline parameters
 */

params {
    // Primary input (file of input files, one per line)
    reads_bam        = null

    // Accessory files
    reference        = null
    reference_index  = null
    reference_dict   = null
    intervals        = null

    // Base name for final output file
    cohort_name      = "my_cohort"
}

docker.fixOwnership = true

profiles {
    docker_on {
        docker.enabled = true
    }
    conda_on {
        conda.enabled = true
    }
    my_laptop {
        process.executor = 'local'
        docker.enabled = true
    }
    univ_hpc {
        process.executor = 'slurm'
        conda.enabled = true
        process.resourceLimits = [
            memory: 750.GB,
            cpus: 200,
            time: 30.d
        ]
    }
    demo {
        // Primary input (file of input files, one per line)
        params.reads_bam        = "${projectDir}/data/sample_bams.txt"

        // Accessory files
        params.reference        = "${projectDir}/data/ref/ref.fasta"
        params.reference_index  = "${projectDir}/data/ref/ref.fasta.fai"
        params.reference_dict   = "${projectDir}/data/ref/ref.dict"
        params.intervals        = "${projectDir}/data/ref/intervals.bed"

        // Base name for final output file
        params.cohort_name      = "family_trio"

        params.outdir           = "results"
    }
}

process {
    // defaults for all processes
    cpus = 2
    memory = 2.GB
    // allocations for a specific process
    withName: 'GATK_JOINTGENOTYPING' {
        cpus = 8
    }
}