Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages


cleanClean up project cache and work directories (Default: last run)
cloneClone a project into a folder
configPrint a project configuration
consoleLaunch Nextflow interactive console
dropDelete the local copy of a project
helpPrint the usage help for a command
infoPrint project and system runtime information
kuberunExecute a workflow in a Kubernetes cluster (experimental)
listList all downloaded projects
logPrint executions log and runtime info
pullDownload or update a project
runExecute a pipeline project
secretsHandle and manage sensitive information for pipeline execution in a safe manner
self-updateUpdate nextflow runtime to the latest available version
viewView project script file(s)


-C <configuration file>Use the specified configuration file(s) overriding any defaults
-D <custom Java system property>Set JVM properties
-bgExecute nextflow in background
-c, -config <configuration file>Add the specified file to configuration set
-d, -dockerizeLaunch nextflow via Docker (experimental)
-hPrint this help
-logSet nextflow log file path
-q, -quietDo not print information messages
-syslogSend logs to syslog server (eg. localhost:514)
-v, -versionPrint the program version