nextflow.config

/*
 *  Copyright (c) 2014-2016, Centre for Genomic Regulation (CRG).
 *  Copyright (c) 2014-2016, Jose Espinosa-Carrasco and the respective authors.
 *
 *  This file is part of Pergola.
 *
 *  Pergola is free software: you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation, either version 3 of the License, or
 *  (at your option) any later version.
 *
 *  Pergola is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with Pergola.  If not, see <http://www.gnu.org/licenses/>.
 */

manifest {
    mainScript = 'N2_vs_case_strain_density.nf'
    description = 'Using data from http://wormbehavior.mrc-lmb.cam.ac.uk/ calculates speed during different motion periods'
}

profiles { 	
	crg { 

		process { 
  			executor = 'crg'
  			queue = 'cn-el7'
			scratch = true
			// This line send mail when something is not working
      			clusterOptions = '-m ae -M jespinosa@ant-login5.linux.crg.es'  
		}	 
		docker.enabled = true
  	}
	cluster {
		process {
			executor = 'sge'
			queue = 'cn-el7'
			scratch = true
			// This line send mail when something is not working
                        clusterOptions = '-m ae -M jespinosa@ant-login5.linux.crg.es'
		}
		docker.enabled = true
	}
 	standard {
  		process {
    			executor = 'local'
    		}
		docker.enabled = true
  	}
}

trace {
	enabled = false
  	trace = false	
    file = 'pipeline_trace.csv'
    fields = 'task_id,name,status,exit,realtime,%cpu,rss'
}

env {
    PATH="/nfs/software/cn/el6.5/python/envs/.virtualenvs/cpython279/bin/pergola_rules.py:$PATH"
}