binac.config

/*
vim: syntax=groovy
-*- mode: groovy;-*-
 * -------------------------------------------------------------
 *  Nextflow config file for use with Singularity on BINAC cluster
 * -------------------------------------------------------------
 * Defines basic usage limits and singularity image id.
 */

singularity {
    enabled = true
}

process {
    beforeScript = 'module load devel/singularity/2.4.1'
    executor = 'pbs'
    queue = 'short'
}

params {
  max_memory = 128.GB
  max_cpus = 28
  max_time = 48.h

    metaFiles {
        'GRCh37' {
            gfasta = '/beegfs/work/zxmai83/Reference/genome/b37/human_g1k_v37.fasta'
            bwa_index = '/beegfs/work/zxmai83/Reference/genome/b37/human_g1k_v37.fasta.bwt'
            dbsnp = '/beegfs/work/zxmai83/Reference/dbs/b37/dbsnp_138.b37.vcf'
            mills = '/beegfs/work/zxmai83/Reference/dbs/b37/Mills_and_1000G_gold_standard.indels.b37.vcf'
            omni = '/beegfs/work/zxmai83/Reference/dbs/b37/1000G_omni2.5.b37.vcf'
            thousandg = '/beegfs/work/zxmai83/Reference/dbs/b37/1000G_phase1.snps.high_confidence.b37.vcf'
        }
    }
    kitFiles {
        'agilent_v5' {
            bait = '/beegfs/work/zxmai83/Reference/kits/agilent_v5/S04380110_Regions.interval_list'
            target = '/beegfs/work/zxmai83/Reference/kits/agilent_v5/S04380110_Covered.interval_list'
            target_bed = '/beegfs/work/zxmai83/Reference/kits/agilent_v5/S04380110_Covered.bed'
        }
        'agilent_v4' {
            bait = '/beegfs/work/zxmai83/Reference/kits/agilent_v4/S04380110_Regions.interval_list'
            target = '/beegfs/work/zxmai83/Reference/kits/agilent_v4/S04380110_Covered.interval_list'
            target_bed = '/beegfs/work/zxmai83/Reference/kits/agilent_v4/S04380110_Covered.bed'
        }
        'agilent_v3' {
            bait = '/beegfs/work/zxmai83/Reference/kits/agilent_v3/Regions.interval_list'
            target = '/beegfs/work/zxmai83/Reference/kits/agilent_v3/Covered.interval_list'
            target_bed = '/beegfs/work/zxmai83/Reference/kits/agilent_v3/Covered.bed'
        }
    }
}