uppmax.config

/*
Uppmax config file for NGI-EXOseq pipeline
Contains paths for meta files, genomes and
configurations for executors i.e. SLURM
*/

process {
    executor = 'slurm'
    cpus = {2 * task.attempt}
    memory = { 16.GB * task.attempt }
    time = { 2.h * task.attempt }
    clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }
    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'finish' }
    maxRetries = 3
    maxErrors = '-1'
    $bwaAlign {
        module = ['bioinfo-tools', 'bwa/0.7.15']
        cpus = { 8 * task.attempt }
        memory = { 64.GB * task.attempt }
        time = { 10.h * task.attempt }
    }
    $fastqToSam {
        module = ['bioinfo-tools', 'picard/2.0.1']
        cpus = { 4 * task.attempt }
    }
    $mergeLaneBam {
        module = ['bioinfo-tools', 'picard/2.0.1']
        cpus = { 8 * task.attempt }
        memory = { 40.GB * task.attempt }
        time = { 10.h * task.attempt }
    }
    $sortLanesBam {
        module = ['bioinfo-tools', 'picard/2.0.1']
    }
    $mergeSampleBam {
        module = ['bioinfo-tools', 'picard/2.0.1']
        cpus = { 8 * task.attempt }
        memory = { 40.GB * task.attempt }
        time = { 10.h * task.attempt }
    }
    $markDuplicate {
        module = ['bioinfo-tools', 'picard/2.0.1']
        cpus = { 8 * task.attempt }
        memory = { 32.GB * task.attempt }
        time = { 5.h * task.attempt }
    }
    $recalibrate {
        module = ['bioinfo-tools', 'GATK/3.7']
        cpus = { 8 * task.attempt }
        memory = { 32.GB * task.attempt }
        time = { 5.h * task.attempt }
    }
    $realign {
        module = ['bioinfo-tools', 'GATK/3.7']
        cpus = { 8 * task.attempt }
        memory = { 32.GB * task.attempt }
        time = { 5.h * task.attempt }
    }
    $calculateMetrics {
        module = ['bioinfo-tools', 'picard/2.0.1']
    }
    $variantCall {
        module = ['bioinfo-tools', 'GATK/3.7']
        cpus = { 8 * task.attempt }
        memory = { 32.GB * task.attempt }
        time = { 8.h * task.attempt }
    }
    $variantSelect {
        module = ['bioinfo-tools', 'GATK/3.7']
        cpus = { 4 * task.attempt }
        time = { 3.h * task.attempt }
    }
    $filterSnp {
        module = ['bioinfo-tools', 'GATK/3.7']
    }
    $filterIndel {
        module = ['bioinfo-tools', 'GATK/3.7']
    }
    $combineVariants {
        module = ['bioinfo-tools', 'GATK/3.7']
        cpus = { 4 * task.attempt }
    }
    $haplotypePhasing {
        module = ['bioinfo-tools', 'GATK/3.7']
        cpus = { 4 * task.attempt }
        time = { 3.h * task.attempt }
    }
    $variantEvaluate {
        module = ['bioinfo-tools', 'GATK/3.7']
        cpus = { 4 * task.attempt }
    }
    $variantAnnotate {
        module = ['bioinfo-tools', 'GATK/3.7', 'snpEff/4.2']
        cpus = { 4 * task.attempt }
        time = { 3.h * task.attempt }
    }
}

params {
    metaFiles {
        'GRCh37' {
            gfasta = '/proj/ngi2016003/nobackup/senthil/seqcap_test/resource/genome_seq_hg19/hg19.fa'
            bwa_index = '/proj/ngi2016003/nobackup/senthil/seqcap_test/resource/bwa_genome_hg19/hg19.ga'
            dbsnp = '/proj/ngi2016003/nobackup/senthil/seqcap_test/resource/training_sets/dbsnp_132.vcf'
            hapmap = '/proj/ngi2016003/nobackup/senthil/seqcap_test/resource/training_sets/hapmap_3.3.vcf'
            omni = '/proj/ngi2016003/nobackup/senthil/seqcap_test/resource/training_sets/1000G_omni2.5.vcf'
        }
    }
    kitFiles {
        'agilent_v5' {
            bait = '/proj/ngi2016003/nobackup/senthil/seqcap_test/resource/agilent_files/SureSelect_Human_All_Exon_V5_baits.interval_list'
            target = '/proj/ngi2016003/nobackup/senthil/seqcap_test/resource/agilent_files/SureSelect_Human_All_Exon_V5_targets.interval_list'
            target_bed = '/proj/ngi2016003/nobackup/senthil/seqcap_test/resource/agilent_files/SureSelect_Human_All_Exon_V5_targets_snpeff.bed'
        }
    }
}