nextflow.config

// Workflow details
manifest {
    author              = 'Alex Di Genova'
    name                = 'call_snv'
    description         = 'Multi sample caller of germline variants from short-reads'
    homePage            = 'https://github.com/digenoma-lab/call_snv'
    }

// Mandate a minimum version of nextflow required to run the pipeline
nextflowVersion     = '!>=20.07.1'

// Set default parameters
params {
wsize=3000000
outdir="results"
debug=false
ref=null
version	          = '1.0'
help		          = false
runstrelka = true
runmanta  = true
rundelly = true

}

// Preset use of containers with Singularity
singularity {
    enabled		    = true
    autoMounts		= true
    }

// Job profiles 
profiles {
    kutral {
        singularity.enabled    = true
        singularity.autoMounts = true
	singularity.runOptions = ' --bind /mnt/beegfs/labs/ '
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
	process.executor = 'slurm'		
	process.queue = 'uohhm'		
    }
} 

// Fail a task if any command returns non-zero exit code
shell = ['/bin/bash', '-euo', 'pipefail']

// Resources for each process 
// default run resource parameters 
process {

withName: 'strelka' {
	cpus    = 80
	memory  = 100.GB
  }

 withName: 'manta' {
        cpus    = 80
        memory = 100.GB
  container     = 'quay.io/biocontainers/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0'                                   
  }
 
}

// Define timestamp, to avoid overwriting existing trace 
def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')

// Produce a workflow diagram
  dag {
    enabled = true
    file = "${params.outdir}/runInfo/svlr_dag_${timestamp}.svg"
  }

  report {
    enabled = true
    file = "${params.outdir}/runInfo/svlr_report_${timestamp}.html"
  }

  timeline {
    enabled = true
    overwrite = true
    file = "${params.outdir}/runInfo/svlr_timeline_${timestamp}.html"
  }

  trace {
    enabled = true
    overwrite = true
    file = "${params.outdir}/runInfo/svlr_trace_${timestamp}.txt"
    fields = 'process,name,status,queue,realtime,cpus,%cpu,memory,%mem,rss,env'
  }