nextflow.md

Configuring Nextflow

Depending on your setup you'll have to adapt the default nextflow.config file.

Executor

You can use the executor configurations as is or tweak them to your own requirements.

executor {
    $sge {
      queueSize = 1000
      pollInterval = '30sec'
      queueStatInterval = '5min'
    }
    $slurm {
      queueSize = 1000
      pollInterval = '30sec'
      queueStatInterval = '5min'
    }
}

Profiles

We've included (and test) a profile for an sge and a slurm environment. You'll probably have to adjust options like 'queue' and 'clusterOptions' to suit your own environment.

profiles {
  sge {
    process.executor = 'sge'
    process.queue = 'all.q' <- change this to your own queue
    process.clusterOptions = '-P cog_bioinf ' <- change this to your own specific cluster options
  }

  slurm {
    process.executor = 'slurm'
    process.queue = 'cpu' <- change this to your own queue
  }
}

Reports

You can use these defaults as is or switch off specific reporting modules by setting enabled to 'false'.

report {
  enabled = true
  file = "$params.out_dir/log/nextflow_report.html"
}

trace {
  enabled = true
  file = "$params.out_dir/log/nextflow_trace.txt"
  fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes,vol_ctxt,inv_ctxt'
}

timeline {
  enabled = true
  file = "$params.out_dir/log/nextflow_timeline.html"

}

Singularity

This workflow requires Singularity and depending on your local setup you'll have to change the runOptions & cacheDir options.

singularity {
  enabled = true
  autoMounts = true
  runOptions = '-B /hpc -B $TMPDIR:$TMPDIR' <- Mount directories /hpc & $TMPDIR inside the Singularity container 
  cacheDir = '/hpc/local/CentOS7/cog_bioinf/singularity_cache' <- Store downloaded singularity images here
}

Cleanup

Clean up the working directory , set to either true or false. Setting it to false is usefull for debugging purposes.

cleanup = true