nextflow.config

params {
    /* Command line parameters */
    bam = "" // The bamfile, on commandline ( --bam )
    runfile = "" // File containing names of multiple bamfiles and out directories on commandline ( --runfile )
    project = "" // Set project or supply on commandline ( --project )
    steps = 'manta,normalize,vep' // Change on commandline --steps x,y,z
    outdir = "results"
    prefix = ''
    help = False

    //optional cohort masking
    sg_mask_ovlp = 0.95 // --sg_mask_ovlp in case other overlap value than default 0.95 for cohort
    no_sg_reciprocal = False // --no_sg_reciprocal in case cohort masking should not include reciprocal overlap option

    // Reference assemblies
    ref_fasta = "/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37/human_g1k_v37.fasta"
    assembly = 'GRCh37'

    // Runtimes for different parts of the workflow
    runtime {
        simple = '3h'    // Short simple shell jobs
        fermikit = '48h' // Fermikit is the longest running of them all
        caller = '24h'  // The rest are a lot quicker
    }

    // Dirs that contain BED files for masking
    mask_artifacts_dir = "$baseDir/mask_artifacts"
    mask_cohort_dir = "$baseDir/mask_cohort"
}

profiles {
    milou {
        includeConfig 'config/standard.config'
        includeConfig 'config/milou.config'
    }

    bianca {
        includeConfig 'config/standard.config'
        includeConfig 'config/bianca.config'
    }

    devel {
        includeConfig 'config/devcore.config'
        includeConfig 'config/milou.config'
    }

    localmilou {
        includeConfig 'config/milou.config'
        process.executor = 'local'
        process.errorStrategy = { $params.runfile != "" ? 'ignore' : 'terminate' }
    }

    localbianca {
        includeConfig 'config/bianca.config'
        process.executor = 'local'
        process.errorStrategy = { $params.runfile != "" ? 'ignore' : 'terminate' }
    }
}

executor {
    $slurm {
        queueSize = 30
    }
    $local {
        queueSize = 30
        cpus = 16
    }
}