SPANDx/nextflow.config at master · dsarov/SPANDx · GitHub

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params {

    fastq                =   "*_{1,2}.fastq.gz"
    ref                  =   "k96243.fasta"
    matrix               =   true
    annotation           =   false
    database		     =   "Burkholderia_pseudomallei_k96243"
    mixtures             =   false
    phylogeny            =   true
	assemblies   	     =   false
    assembly_dir         =   "assemblies/"
	single_end           =   false
    single_end_dir       =   "./single_end/"
	ont                  =   false
	ont_dir              =   "ont"
    window               =   1000
    indels               =   true
    tri_allelic          =   false
    size                 =   0
    phred                =   "-phred33"
    org                  =   "haploid"
    executor             =   "local"
    structural           =   false
    notrim	          	 =   true
    unaligned            =   false
    fast                 =   true
	freebayes            =   false
	snpeff_cache         =   "/home/dereksarovich/miniconda3/envs/spandx/share/snpeff-5.4.0a-0/data"
	snpeff_config        =   "/home/dereksarovich/miniconda3/envs/spandx/share/snpeff-5.4.0a-0/snpEff.config"
}

includeConfig 'configs/gatk.config'
conda.enabled = true

process {

    clusterOptions = "-V"
    executor = params.executor
    clusterOptions = "-A qris-usc"
    clusterOptions = "--partition=general"


    errorStrategy = "retry"
	maxRetries = 4

    withLabel: card {
        cpus = 2
        memory = "4G"
        time = "2h"
    }

    withLabel: index {
        cpus = 2
        memory = "4G"
        time = "2h"
    }

    withLabel: spandx_default {
        cpus = 4
        memory = { 32.GB * task.attempt }
        time = "24h"
    }

    withLabel: spandx_clair3 {
        cpus = 4
        memory = { 16.GB * task.attempt }
        time = "24h"
    }

    withLabel: spandx_alignment {
        cpus = 2
        memory = { 4.GB * task.attempt }
        time = "24h"
    }
    withLabel: spandx_gatk_haplo {
        cpus = 2
        memory = { 4.GB * task.attempt }
        time = "24h"
    }
	withLabel: spandx_gatk {
        cpus = 2
        memory = { 4.GB * task.attempt }
        time = "24h"
    }

    withLabel: spandx_snpeff {
        cpus = 2
        memory = "8G"
        time = "24h"
    }

    withLabel: spandx_pindel {
        cpus = 2
        memory = "8G"
        time = "96h"
    }

    withLabel: bedcov {
        cpus = 2
        memory = "1G"
        time = "1h"
    }

    withLabel: report {
        cpus = 2
        memory = "4G"
        time = "2h"
    }

	withLabel: master_vcf {
        cpus = 2
        memory = { 4.GB * task.attempt }
        time = "24h"
    }
	withLabel: SNP_matrix {
        cpus = 2
        memory = { 4.GB * task.attempt }
        time = "24h"
    }
}

manifest {
    homePage = 'http://github.com/dsarov/SPANDx'
    description = 'A comparative genomics pipeline'
    mainScript = 'main.nf'
    version = '4.0'
}