Command line interface (CLI)

Nextflow provides a robust command line interface for the management and execution pipelines. The top-level interface consists of two aspects, options and commands.

Here’s what you’ll see at the top-level upon invoking the Nextflow CLI:

$ nextflow
Usage: nextflow [options] COMMAND [arg...]

Options

The top-level options are meant to be invoked in relation to the core Nextflow application and are applied to all commands. For options specific to any command, refer the CLI Commands section.

Note

Nextflow options use a single dash prefix, e.g. -foo. Do not confuse with double dash notation, e.g. --foo, which is instead used for Pipeline parameters.

An overview of the top-level options:

$ nextflow
Usage: nextflow [options] COMMAND [arg...]

Options:
-C
    Use the specified configuration file(s) overriding any defaults
-D
    Set JVM properties
-bg
    Execute nextflow in background
-c, -config
    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

Commands...

Hard configuration override

Use the specified configuration file(s) overriding any defaults.

Usage

$ nextflow -C my.config COMMAND [arg...]

Description

The -C option is used to override all settings specified in the default config file. For soft override, please refer the -c option.

Examples

Override any default configuration with a custom configuration file.
```
$ nextflow -C my.config run nextflow-io/hello
```

JVM properties

Set JVM properties.

Usage

$ nextflow -Dkey=value COMMAND [arg...]

Description

This options allows the definition of custom Java system properties that can be used to properly configure or fine tuning the JVM instance used by the Nextflow runtime.

For specifying other JVM level options, please refer to the Environment variables section.

Examples

Add JVM properties to the invoked pipeline.

$ nextflow -Dfile.encoding=UTF-8 run nextflow-io/hello

Execution as a background job

Execute nextflow in the background.

Usage

$ nextflow -bg COMMAND [arg...]

Description

The -bg option is used to invoke the nextflow execution in the background and allows the user to continue interacting with the terminal. This option is similar to nohup in behavior.

Examples

Invoke any execution as a background job.

$ nextflow -bg run nextflow-io/hello

Soft configuration override

Add the specified file to configuration set.

Usage

$ nextflow -c nxf.config COMMAND [arg...]

Description

The -c option is used to append a new configuration to the default configuration. The -c option allows us to update the config in an additive manner. For hard override, refer the -C option.

Examples

Update some fields of the default config for any pipeline.

$ nextflow -c nxf.config run nextflow-io/hello

Docker driven execution

Launch Nextflow via Docker.

Warning

This feature is experimental.

Usage

$ nextflow -dockerize COMMAND [arg...]

Description

The -dockerize option is used to invoke the execution of Nextflow within a Docker container itself without installing a Java VM in the hosting environment.

Note, this option is not needed to run containerised pipeline jobs. For invoking a pipeline with the docker profile or executor, please to refer the -with-docker options the run command.

Examples

Invoke nextflow as a docker container to execute a pipeline.

$ nextflow -dockerize run nextflow-io/hello

Help

Print the help message.

Usage

$ nextflow -h

Description

The -h option prints out the overview of the CLI interface and enumerates the top-level options and commands.

Execution logs

Sets the path of the nextflow log file.

Usage

$ nextflow -log custom.log COMMAND [arg...]

Description

The log option takes a path of the new log file which to be used instead of the default .nextflow.log or to save logs files to another directory.

Examples

Save all execution logs to the custom /var/log/nextflow.log file.

$ nextflow -log /var/log/nextflow.log run nextflow-io/hello

Quiet execution

Disable the printing of information to the terminal.

Usage

$ nextflow -q COMMAND [arg...]

Description

The -q option suppresses the banner, process related info and exits once the execution is completed. Please note that it does not affect any explicit print statement within a pipeline.

Examples

Invoke the pipeline execution without the banner and pipeline information.

$ nextflow -q run nextflow-io/hello

Logging to a syslog server

Send logs to Syslog server endpoint.

Usage

$ nextflow -syslog localhost:1234 COMMAND [arg...]

Description

The -syslog option is used to send logs to a Syslog logging server at the specified endpoint.

Examples

Send the logs to a Syslog server at specific endpoint.

$ nextflow -syslog localhost:1234 run nextflow-io/hello

Version

Print the Nextflow version information.

Usage

$ nextflow -v

Description

The -v option prints out information about Nextflow such as the version and build. The -version option in addition prints out the citation reference and official website.

Examples

The short version.

$ nextflow -v
nextflow version 20.07.1.5412

The full version info with citation and website link.

$ nextflow -version
N E X T F L O W
version 20.07.1 build 5412
created 24-07-2020 15:18 UTC (20:48 IDT)
cite doi:10.1038/nbt.3820
http://nextflow.io

Commands

An overview of the Nextflow top-level commands.

$ nextflow

Usage: nextflow [options] COMMAND [arg...]

Options...

Commands:
clean         Clean up project cache and work directories
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
self-update   Update nextflow runtime to the latest available version
view          View project script file(s)

clean

Clean up cache and work directories.

Usage

$ nextflow clean [run_name|session_id] [options]

Description

Upon invocation within a directory, nextflow creates a project specific .nextflow.log file, .nextflow cache directory as well as a work directory. The clean command is designed to facilitate removal of these files from previous executions. A list of run names and session ids can be generated by invoking nextflow log -q.

If no run name or session id is provided, it will clean the latest run.

Options

Name, shorthand (if any)	Default	Description
-after		Clean up runs executed after the specified one.
-before		Clean up runs executed before the specified one.
-but		Clean up all runs except the specified one.
-dry-run, -n	false	Print names of files to be removed without deleting them.
-force, -f	false	Force clean command.
-help, -h	false	Print the command usage.
-keep-logs, -k	false	Removes only temporary files but retains execution log entries and metadata.
-quiet, -q	false	Do not print names of files removed.

Examples

Dry run to remove work directories for the run name boring_euler:

$ nextflow clean boring_euler -n

Would remove work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
Would remove work/3f/70944c7a549b6221e1ccc7b4b21b62
Would remove work/0e/2ebdba85f76f6068b21a1bcbf10cab

Remove work directories for the run name boring_euler.

$ nextflow clean boring_euler -f

Removed work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
Removed work/3f/70944c7a549b6221e1ccc7b4b21b62
Removed work/0e/2ebdba85f76f6068b21a1bcbf10cab

Remove the execution entries except for a specific execution.

$ nextflow clean -but tiny_leavitt -f

Removed work/1f/f1ea9158fb23b53d5083953121d6b6
Removed work/bf/334115deec60929dc18edf0010032a
Removed work/a3/06521d75da296d4dd7f4f8caaddad8

Dry run to remove the execution data before a specific execution.

$ nextflow clean -before tiny_leavitt -n

Would remove work/5d/ad76f7b7ab3500cf616814ef644b61
Would remove work/c4/69a82b080a477612ba8d8e4c27b579
Would remove work/be/a4fa2aa38f76fd324958c81c2e4603
Would remove work/54/39116773891c47a91e3c1733aad4de

Dry run to remove the execution data after a specific execution.

$ nextflow clean -after focused_payne -n

Would remove work/1f/f1ea9158fb23b53d5083953121d6b6
Would remove work/bf/334115deec60929dc18edf0010032a
Would remove work/a3/06521d75da296d4dd7f4f8caaddad8

Dry run to remove the temporary execution data for a specific execution, while keeping the log files.

$ nextflow clean -keep-logs tiny_leavitt -n

Would remove temp files from work/1f/f1ea9158fb23b53d5083953121d6b6
Would remove temp files from work/bf/334115deec60929dc18edf0010032a
Would remove temp files from work/a3/06521d75da296d4dd7f4f8caaddad8

clone

Clone a remote project into a folder.

Usage

$ nextflow clone [options] [project]

Description

The clone command downloads a pipeline from a Git-hosting platform into the current directory and modifies it accordingly. For downloading a pipeline into the global cache ~/.nextflow/assets, please refer to the nextflow pull command.

Options

Name, shorthand (if any)	Default	Description
-help, -h	false	Print the command usage.
-hub	github	Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
-r	master	Revision to clone - It can be a git `branch`, `tag` or `revision number`
-user		Private repository user name

Examples

Clone the latest revision of a pipeline.

$ nextflow clone nextflow-io/hello
nextflow-io/hello cloned to: hello

Clone a specific revision of a pipeline.

$ nextflow clone nextflow-io/hello -r v1.1
nextflow-io/hello cloned to: hello

config

Print the resolved pipeline configuration.

Usage

$ nextflow config [options] [project name or path]

Description

The config command is used for printing the project’s configuration i.e. the nextflow.config and is especially useful for understanding the resolved profiles and parameters that Nextflow will use run a pipeline. For in-depth information, please refer the Config profiles section.

Options

Name, shorthand (if any)	Default	Description
-flat	false	Print config using flat notation.
-help, -h	false	Print the command usage.
-profile		Choose a configuration profile.
-properties	false	Print config using Java properties notation.
-show-profiles, -a	false	Show all configuration profiles.
-sort	false	Sort config attributes.

Examples

Print out the inferred config using a the default group key-value notation.

$ nextflow config

docker {
    enabled = true
}

process {
    executor = 'local'
}

Print out the config using a flat notation.

$ nextflow config -flat

docker.enabled = true
process.executor = 'local'

Print out the config using the Java properties notation.

$ nextflow config -properties

docker.enabled = true
process.executor = local

Print out all profiles from the project’s configuration.

$ nextflow config -show-profiles

docker {
    enabled = true
}

profiles {
    standard {
        process {
            executor = 'local'
        }
    }
    cloud {
        process {
            executor = 'cirrus'
            container = 'cbcrg/imagex'
        }
    }
}

console

Launch the Nextflow interactive console.

Usage

$ nextflow console

Description

The console command is a wrapper over the Groovy console and provides a Graphic User Interface (GUI) and an interactive REPL (Read-Eval-Print-Loop) for quick experimentation.

Options

None available

Examples

Launch the console GUI.

$ nextflow console

drop

Delete the local copy of a project.

Usage

$ nextflow drop [options] [project]

Description

The drop command is used to remove the projects which have been downloaded into the global cache. Please refer the list command for generating a list of downloaded pipelines.

Options

Name, shorthand (if any)	Default	Description
-f	false	Delete the repository without taking care of local changes.
-help, -h	false	Print the command usage.

Examples

Drop the nextflow-io/hello project.

$ nextflow drop nextflow-io/hello

Forcefully drop the nextflow-io/hello pipeline, ignoring any local changes.

$ nextflow drop nextflow-io/hello -f

help

Print the top-level help or specific help for a command.

Usage

$ nextflow help [options] [command]

Description

The help command prints out the overview of the CLI interface and enumerates the top-level options and commands. Note that this command is equivalent to simply invoking nextflow at the command line.

Options

Name, shorthand (if any)	Default	Description
-help, -h	false	Print the command usage.

Examples

Invoke the help option for the drop command.

$ nextflow help drop

Delete the local copy of a project
Usage: drop [options] name of the project to drop
   Options:
     -f
          Delete the repository without taking care of local changes
          Default: false
     -h, -help
          Print the command usage
          Default: false

info

Print project or system runtime information.

Usage

$ nextflow info [options] [project]

Description

The info command prints out the nextflow runtime information about the hardware as well as the software versions of the Nextflow version and build, Operating System and Groovy and Java runtime. It can also be used to display information about a specific project.

Options

Name, shorthand (if any)	Default	Description
-check-updates, -u	false	Check for remote updates.
-d	false	Show detailed information.
-help, -h	false	Print the command usage.
-o	text	Output format, either `text`, `json` or `yaml`.

Examples

Display Nextflow runtime and system info:

$ nextflow info

  Version: 20.07.1 build 5412
  Created: 24-07-2020 15:18 UTC (20:48 IDT)
  System: Mac OS X 10.15.6
  Runtime: Groovy 2.5.11 on OpenJDK 64-Bit Server VM 1.8.0_192-b01
  Encoding: UTF-8 (UTF-8)

Display information about a specific project:

$ nextflow info nextflow-io/hello

  project name: nextflow-io/hello
  repository  : https://github.com/nextflow-io/hello
  local path  : /Users/evanfloden/.nextflow/assets/nextflow-io/hello
  main script : main.nf
  revisions   :
  * master (default)
    mybranch
    testing
    v1.1 [t]
    v1.2 [t]

kuberun

Deploy Nextflow into a Kubernetes cluster (experimental)

Usage

$ nextflow kuberun [options] [project]

Description

The kuberun command builds upon the run command and offers a deep integration with the Kubernetes execution environment. This command deploys the Nextflow runtime as a Kubernetes pod and assumes that you’ve already installed the kubectl CLI. The kuberun command does not allow the execution of local Nextflow scripts. For more information please refer the Kubernetes section.

Options

Name, shorthand (if any)	Default	Description
-E	false	Exports all current system environment.
-ansi-log		Enable/disable ANSI console logging.
-bucket-dir		Remote bucket where intermediate result files are stored.
-cache		Enable/disable processes caching.
-disable-jobs-cancellation		Prevent the cancellation of child jobs on execution termination
-dsl1	false	Execute the workflow using DSL1 syntax.
-dsl2	false	Execute the workflow using DSL2 syntax.
-dump-channels		Dump channels for debugging purpose.
-dump-hashes	false	Dump task hash keys for debugging purpose.
-e.	{}	Add the specified variable to execution environment. Syntax: `-e.key=value`
-entry		Entry workflow name to be executed.
-head-cpus	0	Specify number of CPUs requested for the Nextflow pod
-head-memory		Specify amount of memory requested for the Nextflow pod
-h, -help	false	Print the command usage.
-hub	github	Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
-latest	false	Pull latest changes before run.
-lib		Library extension path.
-main-script		The script file to be executed when launching a project directory or repository
-name		Assign a mnemonic name to the a pipeline run.
-n, -namespace		Specify the K8s namespace to use.
-offline	false	Do not check for remote project updates.
-params-file		Load script parameters from a JSON/YAML file.
-plugins		Specify the plugins to be applied for this run e.g. nf-amazon,nf-tower
-pod-image		Specify the container image for the Nextflow pod
-head-image		Specify the container image for the Nextflow driver pod
-preview		Run the workflow script skipping the execution of all processes
-process.	{}	Set process options. Syntax `-process.key=value`
-profile		Choose a configuration profile.
-qs, -queue-size		Max number of processes that can be executed in parallel by each executor.
-remoteConfig		Add the specified file from the K8s cluster to configuration set.
-remoteProfile		Choose a configuration profile in the remoteConfig.
-resume		Execute the script using the cached results, useful to continue executions that was stopped by an error.
-r, -revision		Revision of the project to run (either a git branch, tag or commit SHA number). When passing a git tag or branch, the `workflow.revision` and the associated `workflow.commitId` is populated. When passing only the commit ID, no `workflow.revision` is returned.
-stub, -stub-run		Execute the workflow replacing process scripts with command stubs.
-test		Test a script function with the name specified.
-user		Private repository user name.
-v, -volume-mount		Volume claim mounts eg. `my-pvc:/mnt/path`
-with-charliecloud		Enable process execution in a Charliecloud container runtime
-with-conda		Use the specified Conda environment package or file (must end with `.yml\|.yaml`)
-with-dag	dag.dot	Create pipeline DAG file.
-with-docker		Enable process execution in a Docker container.
-N, -with-notification		Send a notification email on workflow completion to the specified recipients.
-with-podman		Enable process execution in a Podman container.
-with-report	report.html	Create processes execution html report.
-with-spack		Use the specified Spack environment package or file (must end with `.yaml`)
-with-singularity		Enable process execution in a Singularity container.
-with-timeline	timeline.html	Create processes execution timeline file.
-with-tower		Monitor workflow execution with Seqera Tower service.
-with-trace	trace.txt	Create processes execution tracing file.
-with-wave		Enable the use of Wave containers service.
-with-weblog		Send workflow status messages via HTTP to target URL.
-without-conda	false	Disable process execution with Conda.
-without-docker	false	Disable process execution with Docker.
-without-podman		Disable process execution in a Podman container.
-without-spack	false	Disable process execution with Spack.
-without-wave		Disable the use of Wave containers service.
-w, -work-dir	work	Directory where intermediate result files are stored.

Examples

Execute a pipeline into a Kubernetes cluster.

$ nextflow kuberun nextflow-io/hello

list

List all downloaded projects.

Usage

$ nextflow list [options]

Description

The list commands prints a list of the projects which are already downloaded into the global cache ~/.nextflow/assets.

Options

Name, shorthand (if any)	Default	Description
-help, -h	false	Print the command usage.

Examples

List the downloaded pipelines.

$ nextflow list

nextflow-io/hello
nextflow-hub/fastqc

log

Print the execution history and log information.

Usage

$ nextflow log [options] [run_name | session_id]

Description

The log command is used to query the execution metadata associated with pipelines executed by Nextflow. The list of executed pipelines can be generated by issuing nextflow log at the terminal. Instead of run name, it’s also possible to use a session id. Moreover, this command contains multiple options to facilitate the queries and is especially useful while debugging a pipeline and while inspecting pipeline execution metadata.

Options

Name, shorthand (if any)	Default	Description
-after		Show log entries for runs executed after the specified one.
-before		Show log entries for runs executed before the specified one.
-but		Show log entries for runs executed but the specified one.
-fields, -f		Comma separated list of fields to include in the printed log.
-filter, -F		Filter log entries by a custom expression e.g. `process =~ /foo.*/ && status == 'COMPLETED'`
-help, -h	false	Print the command usage.
-list-fields, -l	false	Show all available fields.
-quiet	false	Show only run names.
-s		Character used to separate column values
-template, -t		Text template used to each record in the log.

Examples

Listing the execution logs of previous invocations of all pipelines in a project.

$ nextflow log

TIMESTAMP           DURATION        RUN NAME        STATUS  REVISION ID     SESSION ID                              COMMAND
2020-10-07 11:52:24 2.1s            focused_payne   OK      96eb04d6a4      af6adaaa-ad4f-48a2-9f6a-b121e789adf5    nextflow run nextflow-io/hello -r master
2020-10-07 11:53:00 3.1s            tiny_leavitt    OK      e3b475a61b      4d3b95c5-4385-42b6-b430-c865a70d56a4    nextflow run ./tutorial.nf
2020-10-07 11:53:29 2.5s            boring_euler    OK      e3b475a61b      a6276975-7173-4208-ae09-ab9d6dce8737    nextflow run tutorial.nf

Listing only the run names of the execution logs of all pipelines invocations in a project.

$ nextflow log -quiet

focused_payne
tiny_leavitt
boring_euler

List the execution entries only a specific execution.

$ nextflow log tiny_leavitt

work/1f/f1ea9158fb23b53d5083953121d6b6
work/bf/334115deec60929dc18edf0010032a
work/a3/06521d75da296d4dd7f4f8caaddad8

List the execution entries after a specific execution.

$ nextflow log -after tiny_leavitt

work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
work/3f/70944c7a549b6221e1ccc7b4b21b62
work/0e/2ebdba85f76f6068b21a1bcbf10cab

List the execution entries before a specific execution.

$ nextflow log -before tiny_leavitt

work/5d/ad76f7b7ab3500cf616814ef644b61
work/c4/69a82b080a477612ba8d8e4c27b579
work/be/a4fa2aa38f76fd324958c81c2e4603
work/54/39116773891c47a91e3c1733aad4de

List the execution entries except for a specific execution.

$ nextflow log -but tiny_leavitt

 work/5d/ad76f7b7ab3500cf616814ef644b61
 work/c4/69a82b080a477612ba8d8e4c27b579
 work/be/a4fa2aa38f76fd324958c81c2e4603
 work/54/39116773891c47a91e3c1733aad4de

Filter specific fields from the execution log of a process.

$ nextflow log tiny_leavitt -f 'process,exit,hash,duration'

splitLetters        0       1f/f1ea91       112ms
convertToUpper      0       bf/334115       144ms
convertToUpper      0       a3/06521d       139ms

Filter fields from the execution log of a process based on a criteria.

$ nextflow log tiny_leavitt -F 'process =~ /splitLetters/'

work/1f/f1ea9158fb23b53d5083953121d6b6

pull

Download or update a project.

Usage

$ nextflow pull [options] [project]

Description

The pull command downloads a pipeline from a Git-hosting platform into the global cache ~/.nextflow/assets and modifies it accordingly. For downloading a pipeline into a local directory, please refer to the nextflow clone command.

Options

Name, shorthand (if any)	Default	Description
-all	false	Update all downloaded projects.
-help, -h	false	Print the command usage.
-hub	github	Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
-r, -revision		Revision of the project to run (either a git branch, tag or commit SHA number). When passing a git tag or branch, the `workflow.revision` and the associated `workflow.commitId` is populated. When passing only the commit ID, no `workflow.revision` is returned.
-user		Private repository user name

Examples

Download a new pipeline or pull the latest revision for a specific project.

$ nextflow pull nextflow-io/hello

Checking nextflow-io/hello ...
done - revision: 96eb04d6a4 [master]

Pull the latest revision for all downloaded projects.

$ nextflow pull -all

Checking nextflow-io/hello ...
done - revision: 96eb04d6a4 [master]
Checking nextflow-hub/fastqc ...
done - revision: 087659b18e [master]

Download a specific revision of a new project or pull the latest revision for a specific project.

$ nextflow pull nextflow-io/hello -r v1.1

Checking nextflow-io/hello ...
checkout-out at AnyObjectId[1c3e9e7404127514d69369cd87f8036830f5cf64] - revision: 1c3e9e7404 [v1.1]

run

Execute a pipeline.

Usage

$ nextflow run [options] [project]

Description

The run command is used to initiate the execution of the a pipeline script or download a pipeline project. Along with serving the purpose of script execution, this command facilitates rapid iterations, inspections of any pipeline as well as debugging.

Options

Name, shorthand (if any)	Default	Description
-E	false	Exports all current system environment.
-ansi-log		Enable/disable ANSI console logging.
-bucket-dir		Remote bucket where intermediate result files are stored.
-cache		Enable/disable processes caching.
-disable-jobs-cancellation		Prevent the cancellation of child jobs on execution termination
-dsl1	false	Execute the workflow using DSL1 syntax.
-dsl2	true	Execute the workflow using DSL2 syntax.
-dump-channels		Dump channels for debugging purpose.
-dump-hashes	false	Dump task hash keys for debugging purpose.
-e.	{}	Add the specified variable to execution environment. Syntax: `-e.key=value`
-entry		Entry workflow name to be executed.
-h, -help	false	Print the command usage.
-hub	github	Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
-latest	false	Pull latest changes before run.
-lib		Library extension path.
-main-script	main.nf	The script file to be executed when launching a project directory or repository (requires version 20.09.1-edge or later).
-name		Assign a mnemonic name to the a pipeline run.
-offline	false	Do not check for remote project updates.
-params-file		Load script parameters from a JSON/YAML file.
-plugins		Comma separated list of plugin ids to be applied in the pipeline execution.
-process.	{}	Set process options. Syntax `-process.key=value`
-profile		Choose a configuration profile.
-qs, -queue-size		Max number of processes that can be executed in parallel by each executor.
-resume		Execute the script using the cached results, useful to continue executions that was stopped by an error.
-r, -revision		Revision of the project to run (either a git branch, tag, or commit SHA number) When passing a git tag or branch, the `workflow.revision` and the associated `workflow.commitId` is populated. When passing only the commit ID, no `workflow.revision` is returned.
-stub-run, -stub	false	Execute the workflow replacing process scripts with command stubs
-test		Test a script function with the name specified.
-user		Private repository user name.
-with-charliecloud		Enable process execution in a Charliecloud container runtime
-with-conda		Use the specified Conda environment package or file (must end with `.yml\|.yaml`)
-with-dag	dag.dot	Create pipeline DAG file.
-with-docker		Enable process execution in a Docker container.
-N, -with-notification		Send a notification email on workflow completion to the specified recipients.
-with-podman		Enable process execution in a Podman container.
-with-report	report.html	Create processes execution html report.
-with-singularity		Enable process execution in a Singularity container.
-with-spack		Use the specified Spack environment package or file (must end with `.yaml`)
-with-timeline	timeline.html	Create processes execution timeline file.
-with-tower		Monitor workflow execution with Seqera Tower service.
-with-trace	trace.txt	Create processes execution tracing file.
-with-weblog		Send workflow status messages via HTTP to target URL.
-without-docker	false	Disable process execution with Docker.
-without-podman		Disable process execution in a Podman container.
-w, -work-dir	work	Directory where intermediate result files are stored.

Examples

Run a specific revision of a downloaded pipeline.

$ nextflow run nextflow-io/hello -r v1.1

N E X T F L O W  ~  version 20.07.1
Launching `nextflow-io/hello` [grave_cajal] - revision: 1c3e9e7404 [v1.1]

Choose a profile for running the project. Assumes that a profile named docker has already been defined in the config file.
```
$ nextflow run main.nf -profile docker
```
Invoke the pipeline execution and generate the summary HTML report. For more information on the metrics, please refer the Tracing & visualisation section:
```
$ nextflow run main.nf -with-report
```
Invoke the nextflow pipeline execution with a custom queue size. By default, the value of queue-size is the same as the number of available CPUs.
```
$ nextflow run nextflow-io/hello -qs 4
```
Execute the pipeline with DSL-2 syntax.
```
$ nextflow run nextflow-io/hello -dsl2
```
Invoke the pipeline with a specific workflow as the entry-point, this option is meant to be used with DSL-2. For more information on DSL-2, please refer to DSL 2
```
$ nextflow run main.nf -entry workflow_A
```
Invoke the nextflow pipeline execution with the integrated monitoring dashboard Tower. For more information, please refer to the tower.nf website.
```
$ nextflow run nextflow-io/hello -with-tower
```
Invoke the nextflow pipeline execution with a custom parameters YAML/JSON file.:
```
$ nextflow run main.nf -params-file pipeline_params.yml
```
For example, the following params file in YAML format:
```
alpha: 1
beta: 'foo'
```
Or in JSON format:
```
{
  "alpha": 1,
  "beta": "foo"
}
```
Is equivalent to this command in CLI:
```
$ nextflow run main.nf --alpha 1 --beta foo
```
The parameters specified with this mechanism are merged with the resolved configuration (base configuration and profiles). The values provided via a params file overwrite those of the same name in the Nextflow configuration file.

self-update

Update the nextflow runtime to the latest available version.

Usage

$ nextflow self-update

Description

The self-update command directs the nextflow cli to update itself to the latest stable release.

Examples

Update Nextflow.

$ nextflow self-update

      N E X T F L O W
      version 20.07.1 build 5412
      created 24-07-2020 15:18 UTC (20:48 IDT)
      cite doi:10.1038/nbt.3820
      http://nextflow.io


Nextflow installation completed. Please note:
- the executable file `nextflow` has been created in the folder: /usr/local/bin

view

View a project’s script file(s).

Usage

$ nextflow view [options] [project]

Description

The view command is used to inspect the pipelines that are already stored in the global nextflow cache. For downloading a pipeline into the global cache ~/.nextflow/assets, refer to the pull command.

Options

Name, shorthand (if any)	Default	Description
-help, -h	false	Print the command usage.
-l	false	List repository content.
-q	false	Hide header line.

Examples

Viewing the contents of a downloaded pipeline.

$ nextflow view nextflow-io/hello

== content of file: .nextflow/assets/nextflow-io/hello/main.nf
#!/usr/bin/env nextflow
nextflow.enable.dsl=2

process sayHello {
  input:
    val x
  output:
    stdout
  script:
    """
    echo '$x world!'
    """
}

workflow {
  Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
}

List the folder structure of the downloaded pipeline.

$ nextflow view -l nextflow-io/hello

== content of path: .nextflow/assets/nextflow-io/hello
LICENSE
README.md
nextflow.config
.gitignore
circle.yml
foo.nf
.git
.travis.yml
main.nf

View the contents of a downloaded pipeline without omitting the header.

$ nextflow view -q nextflow-io/hello

#!/usr/bin/env nextflow
nextflow.enable.dsl=2

process sayHello {
  input:
    val x
  output:
    stdout
  script:
    """
    echo '$x world!'
    """
}

workflow {
  Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
}

Pipeline parameters

Pipeline scripts can use an arbitrary number of parameters that can be overridden, either using the command line or the Nextflow configuration file. Any script parameter can be specified on the command line, prefixing the parameter name with double dash characters, e.g.:

nextflow run <my script> --foo Hello

Then, the parameter can be accessed in the pipeline script using the params.foo identifier.

Note

When the parameter name is formatted using camelCase, a second parameter is created with the same value using kebab-case, and vice versa.

Warning

When a command line parameter includes one or more glob characters, i.e. wildcards like * or ?, the parameter value must to be enclosed in quotes to prevent Bash expansion and preserve the glob characters. For example:

nextflow run <my script> --files "*.fasta"