nextflow.config

docker {
    enabled = true
    temp = 'auto'
    runOptions = '-u $(id -u):$(id -g)'
}

executor {
  name = 'local'
  cpus = 30
  memory = '150 GB'
}


params {
    bed                         =       "$baseDir/bin/primer_v4.1.bed"
    prefix_fasta                =       "PH-RITM-"
    trace_dir                   =       "${params.out_dir}/pipeline_info"
    usherDB                     =       "$baseDir/assets/NC_045512v2.fasta"
    usherProblemSites           =       "$baseDir/assets/problematic_sites_sarsCov2.vcf"
    usherGlobalLineages         =       "http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/public-latest.all.masked.pb.gz"
}



// Information on the pipeline and its execution
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.trace_dir}/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.trace_dir}/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.trace_dir}/execution_trace_${trace_timestamp}.txt"
}
dag {
    enabled = true
    file    = "${params.trace_dir}/pipeline_dag_${trace_timestamp}.svg"
}