nextflow.config

nextflow.enable.dsl=1

env {
  PYTHONNOUSERSITE = 1
}

manifest {
    mainScript = 'as_rnaseq.nf'
}
 
includeConfig "$baseDir/params.config"

profiles {
	local {
    	process {
   		 	container = 'biocorecrg/asrnaseq:0.3'
    		executor = 'local'
    		cpus = 1
    		memory = '7GB' 
    	}  
    } 
	standard {
		process {
 	       container = 'biocorecrg/asrnaseq:0.3'
    	 	queue='biocore-el7,long-centos79,short-centos79'
     		memory='12G'
     		cpus='1'
     		time='6h'
   			withLabel: long_mem {
            	 time='24h'
           	     memory='40G'
                 cpus='1'
        	}
       		withLabel: big_comp { 
    	        time='6h'
   				memory='60G'
   	 			cpus='8'
   	 		}
		} 
	}

       slurm {
               process {
               container = 'biocorecrg/asrnaseq:0.3'
               queue='genoa64'
               executor = "slurm"
               clusterOptions = { task.time <= 3.h ? '--qos=shorter' :
                 (task.time <= 6.h ? '--qos=short' :
                 (task.time <= 12.h ? ' --qos=normal' :
                 (task.time <= 24.h ? '--qos=long' :
                 (task.time <= 48.h ? '--qos=vlong' : '--qos=marathon' )))) }

                memory='12G'
                cpus='1'
                time='6h'
                        withLabel: long_mem {
                 time='24h'
                     memory='40G'
                 cpus='1'
                }
                withLabel: big_comp {
                time='6h'
                                memory='60G'
                                cpus='8'
                        }
                }
        }

}

//singularity.cacheDir = "$baseDir/singularity"
//singularity.enabled = true