nextflow.config

#!/usr/bin/env nextflow

/*
 * -------------------------------------------------
 *  amchakra/tosca config file
 * -------------------------------------------------
 * Main config
 */


// Main parameters
params {
  // General
  outdir = './results'
  tracedir = "${params.outdir}/pipeline_info"
  keep_intermediates = true  
  keep_cache = true 
  verbose = false

  multiqc_config = "${projectDir}/assets/multiqc_config.yaml"
}

// Enable by default nextflow tracing and place in trace dir location
timeline {
  enabled = true
  file = "${params.tracedir}/execution_timeline.html"
}
report {
  enabled = true
  file = "${params.tracedir}/execution_report.html"
}
trace {
  enabled = true
  file = "${params.tracedir}/execution_trace.txt"
  fields = "task_id,hash,native_id,name,status,exit,submit,start,complete,duration,realtime,cpus,time,memory,%cpu,peak_rss,peak_vmem,rchar,wchar"
}
dag {
  enabled = true
  file = "${params.tracedir}/pipeline_dag.svg"
}

// Include other configs
includeConfig 'conf/genomes.config'
includeConfig 'conf/defaults.config'

// Create run profiles
profiles {
  test { includeConfig 'conf/test.config'}
  github { includeConfig 'conf/github.config'}
  crick { includeConfig 'conf/crick.config' }
  docker {
    docker.enabled = true
  }
  singularity {
    singularity.enabled = true
    singularity.autoMounts = true
  }
}

// Needs to be after profiles for if statements
includeConfig 'conf/resources.config'

// Container slug. Stable releases should specify release tag!
process.container = 'amchakrabarti/tosca:1.0.0'

// Static details about the pipeline
manifest {
  name = 'amchakra/tosca'
  author = 'A. M. Chakrabarti'
  homePage = 'https://github.com/amchakra/tosca'
  description = 'A Nextflow hiCLIP/proximity ligation analysis pipeline'
  nextflowVersion = '>=20.07.01'
  version = '1.0.0'
}

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

// Avoid this error:
// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. 
// Memory limited without swap.
// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351, 
//once this is established and works well, nextflow might implement this behavior as new default.
docker.runOptions = '-u \$(id -u):\$(id -g)'