nextflow.config

/*
Nextflow configuration file for SNPmatch on GMI Mendel

please edit config file if you want to implement to another cluster

*/
params {
  version = '5.0.0' // Pipeline version
  nf_required_version = '19.04.0' // Minimum version of nextflow required
}


profiles {
  standard {
    includeConfig 'conf/cbe.config'
  }
  mendel {
    includeConfig 'conf/mendel.config'
  }
  local { process.executor = 'local' }
}

process {

  errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
  maxRetries = 3
  maxErrors = '-1'

  container = 'docker.artifactory.imp.ac.at/nordborglab/snpmatch:master'
  // conda = "$HOME/.conda/envs/snpmatch"
  cpus = 1
  memory = 10.GB
  time = 6.h

}

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
  PYTHONNOUSERSITE = 1
  R_PROFILE_USER = "/.Rprofile"
  R_ENVIRON_USER = "/.Renviron"
}


// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
  enabled = true
  file = "${params.outdir}/pipeline_info/snpmatch_timeline.html"
}
report {
  enabled = true
  file = "${params.outdir}/pipeline_info/snpmatch_report.html"
}
trace {
  enabled = true
  file = "${params.outdir}/pipeline_info/snpmatch_trace.txt"
}
dag {
  enabled = true
  file = "${params.outdir}/pipeline_info/snpmatch_dag.svg"
}