gadi.config

// Set gadi parameters
// NCI has special install of Nextflow. See: https://opus.nci.org.au/display/DAE/Nextflow

// NOT CURRENTLY IN USE //

// See https://www.nextflow.io/docs/latest/config.html#scope-params 
params {
	gadi_account = System.getenv("PROJECT")
	storage_account = ''
	whoami = ''
	singularityCacheDir = ''
}

// Autodetect relevant Singularity env variables 
singularity {
	enabled = true
	autoMounts = true
	autoCleanUp = true
	cacheDir = "/scratch/${params.gadi_account}/${params.whoami}/singularity"

// Autodetect Singularity libraryDir. See: https://nextflow.io/docs/edge/container.html#singularity-docker-hub 
	//libraryDir = params.singularityCacheDir ? params.singularityCacheDir
  //      : "/scratch/${params.gadi_account}/${params.whoami}/.nextflow/singularity"		
	//temp = "/scratch/${params.gadi_account}/${params.whoami}/.nextflow/singularity/temp"	
}

// Set default resources for each process 
// See https://www.nextflow.io/docs/latest/config.html?highlight=withname#scope-process 
process {
	module = 'singularity'
	cache = 'lenient'
	executor = 'pbspro'
  project = "${params.gadi_account}"
	storage = "${params.gadi_storage}"

}

// Write custom trace file with outputs required for SU calculation
def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
trace {
    enabled = true
    overwrite = false
    file = "${params.outdir}/run_info/gadi-nf-core-trace-${trace_timestamp}.txt"
    fields = 'name,status,exit,duration,realtime,cpus,%cpu,memory,%mem,rss'
}