nextflow

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

Subcommands

Name	Description
`clean`	Clean up project cache and work directories (Default: last run)
`clone`	Clone a project into a folder
`config`	Print a project configuration
`console`	Launch Nextflow interactive console
`drop`	Delete the local copy of a project
`help`	Print the usage help for a command
`info`	Print project and system runtime information
`kuberun`	Execute a workflow in a Kubernetes cluster (experimental)
`list`	List all downloaded projects
`log`	Print executions log and runtime info
`pull`	Download or update a project
`run`	Execute a pipeline project
`secrets`	Handle and manage sensitive information for pipeline execution in a safe manner
`self-update`	Update nextflow runtime to the latest available version
`view`	View project script file(s)

Options

Name	Description
`-C <configuration file>`	Use the specified configuration file(s) overriding any defaults
`-D <custom Java system property>`	Set JVM properties
`-bg`	Execute nextflow in background
`-c, -config <configuration file>`	Add the specified file to configuration set
`-d, -dockerize`	Launch nextflow via Docker (experimental)
`-h`	Print this help
`-log`	Set nextflow log file path
`-q, -quiet`	Do not print information messages
`-syslog`	Send logs to syslog server (eg. localhost:514)
`-v, -version`	Print the program version