nextflow.config

/*
vim: syntax=groovy
-*- mode: groovy;-*-
 * -------------------------------------------------
 *  NGI-RNAfusion Nextflow config file
 * -------------------------------------------------
 * Default config options for all environments.
 * Cluster-specific config options should be saved
 * in the conf folder and imported under a profile
 * name here.
 */

// Variable to specify the docker / singularity image tag to use
// Picks up on use of -r 1.3 in nextflow command
wf_container = { "scilifelab/ngi-rnafusion:${workflow.revision ? workflow.revision : 'latest'}" }

profiles {
  standard {
    includeConfig 'conf/base.config'
    includeConfig 'conf/uppmax.config'
  }
  docker {
    includeConfig 'conf/base.config'
    includeConfig 'conf/docker.config'
  }
  upgrade {
    includeConfig 'conf/base.config'
    includeConfig 'conf/singularity.config'
  }
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

params.outdir = './results'
timeline {
  enabled = true
  file = "${params.outdir}/NGI-RNAfusion_timeline.html"
}
trace {
  enabled = true
  file = "${params.outdir}/NGI-RNAfusion_trace.txt"
}

manifest {
  homePage = 'https://github.com/SciLifeLab/NGI-RNAfusion'
  description = 'Nextflow RNA gene fusion detection Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.'
}