nextflow.config

params {
	
	// WORKFLOW PARAMETERS TO REVIEW AT EACH RUN
	// ----------------------------------------
	
	// Where to place results
	results = "$launchDir/results"
	
	
	// WORKFLOW PARAMETERS THAT SHOULD NOT BE CHANGED
	// ----------------------------------------
	
	
}


// WHETHER TO GENERATE A REPORT OF RUN STATISTICS
report {
  enabled = true
  file    = "${params.results}/report.html"
}


// WHETHER TO GENERATE A VISUALIZATION OF THE WORKFLOW
dag {
	enabled = true
	overwrite = true
	file = 'workflow-visualization.png'
}


// WHETHER TO REMOVE TEMPORARY FILES AFTER A SUCCESSFUL RUN
cleanup = false


// PROFILE OPTIONS
profiles {
	
	standard {
		
		docker.enabled = true
		singularity.enabled = false
		conda.enabled = false
		
		process {
			
			withName:PROCESS_NAME {
				container = ""
			}
		}
		
	}
	
	docker {
		
		docker.enabled = true
		singularity.enabled = false
		conda.enabled = false
		
		process {
			
			withName:PROCESS_NAME {
				container = ""
			}
		}
		
	}
	
	singularity {
		
		singularity.enabled = true
		docker.enabled = false
		conda.enabled = false
		
		process {
			
			withName:PROCESS_NAME {
				container = ""
			}
		}
		
	}
	
	conda {
		
		conda {
			enabled = true
			// cacheDir = "$baseDir/config/envs"
			// createOptions = "-y -c conda-forge -c bioconda -c r"
			useMamba = true
		}
		
		singularity.enabled = false
		docker.enabled = false
		
		process {
			
			withName:PROCESS_NAME {
				conda = ""
			}
		}
		
	}
}


// MANIFEST
manifest {
	homePage = ''
	mainScript = 'main.nf'
	defaultBranch = 'main'
	description = ''
	author = ''
}