Environment variables

The following environment variables control the configuration of the Nextflow runtime and the underlying Java virtual machine.

Java settings

JAVA_CMD

Defines the path location of the Java binary command used to launch Nextflow.

JAVA_HOME

Defines the path location of the Java VM installation used to run Nextflow.

Nextflow settings

NXF_ANSI_LOG

Enables/disables ANSI console output (default true when ANSI terminal is detected).

NXF_ANSI_SUMMARY

Enables/disables ANSI completion summary: true\|false (default: print summary if execution last more than 1 minute).

NXF_ASSETS

Defines the directory where downloaded pipeline repositories are stored (default: $NXF_HOME/assets)

NXF_CACHE_DIR

New in version 24.02.0-edge.

Defines the base cache directory when using the default cache store (default: "$launchDir/.nextflow").

NXF_CHARLIECLOUD_CACHEDIR

Directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.

NXF_CLOUDCACHE_PATH

New in version 23.07.0-edge.

Defines the base cache path when using the cloud cache store.

NXF_CLOUD_DRIVER

Defines the default cloud driver to be used if not specified in the config file or as command line option, either aws or google.

NXF_CONDA_CACHEDIR

Directory where Conda environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.

NXF_CONDA_ENABLED

New in version 22.08.0-edge.

Enable the use of Conda recipes defined by using the conda directive. (default: false).

NXF_CONTAINER_ENTRYPOINT_OVERRIDE

Deprecated since version 22.10.0.

When true, override the container entrypoint with /bin/bash (default: false).

NXF_DATE_FORMAT

New in version 25.07.0-edge.

Defines the format for date and time representations in notifications and reports. Supports custom formats (e.g., yyyy-MM-dd HH:mm:ss) or iso for ISO 8601 format with timezone (default: dd-MMM-yyyy HH:mm:ss).

NXF_DEFAULT_DSL

New in version 22.03.0-edge.

Defines the DSL version that should be used in not specified otherwise in the script of config file (default: 2)

NXF_DISABLE_CHECK_LATEST

New in version 23.09.0-edge.

Nextflow automatically checks for a newer version of itself unless this option is enabled (default: false).

NXF_DISABLE_JOBS_CANCELLATION

New in version 21.12.0-edge.

Disables the cancellation of child jobs on workflow execution termination.

NXF_DISABLE_PARAMS_TYPE_DETECTION

New in version 23.07.0-edge.

Disables the automatic type detection of command line parameters.

NXF_DISABLE_WAVE_SERVICE

New in version 23.08.0-edge.

Disables the requirement for Wave service when enabling the Fusion file system.

NXF_ENABLE_AWS_SES

New in version 23.06.0-edge.

Enable to use of AWS SES native API for sending emails in place of legacy SMTP settings (default: false)

NXF_ENABLE_FS_SYNC

New in version 23.10.0.

When enabled the job script will execute Linux sync command on job completion. This may be useful to synchronize the job state over shared file systems (default: false)

NXF_ENABLE_SECRETS

New in version 21.09.0-edge.

Enable Nextflow secrets features (default: true)

NXF_ENABLE_STRICT

New in version 22.05.0-edge.

Enable Nextflow strict execution mode (default: false)

NXF_ENABLE_VIRTUAL_THREADS

New in version 23.05.0-edge.

Enable the use of virtual threads in the Nextflow runtime (default: false)

NXF_EXECUTOR

Defines the default process executor, e.g. sge

NXF_FILE_ROOT

New in version 23.05.0-edge.

The file storage path against which relative file paths are resolved.

For example, with NXF_FILE_ROOT=/some/root/path, the use of file('hello') will be resolved to the absolute path /some/root/path/hello. A remote root path can be specified using the usual protocol prefix, e.g. NXF_FILE_ROOT=s3://my-bucket/data. Files defined using an absolute path are not affected by this setting.

NXF_HOME

Nextflow home directory (default: $HOME/.nextflow).

NXF_JAVA_HOME

Defines the path location of the Java VM installation used to run Nextflow. This variable overrides the JAVA_HOME variable if defined.

NXF_JVM_ARGS

New in version 21.12.1-edge.

Allows the setting Java VM options. This is similar to NXF_OPTS however it’s only applied the JVM running Nextflow and not to any java pre-launching commands.

NXF_LOG_FILE

The filename of the Nextflow log (default: .nextflow.log)

NXF_OFFLINE

When true prevents Nextflow from automatically downloading and updating remote project repositories (default: false).

Changed in version 23.09.0-edge: This option also disables the automatic version check (see NXF_DISABLE_CHECK_LATEST).

Changed in version 23.11.0-edge: This option also prevents plugins from being downloaded. Plugin versions must be specified in offline mode, or else Nextflow will fail.

NXF_OPTS

Provides extra options for the Java and Nextflow runtime. It must be a blank separated list of -Dkey[=value] properties.

NXF_ORG

Default organization prefix when looking for a hosted repository (default: nextflow-io).

NXF_PARAMS_FILE

New in version 20.10.0.

Defines the path location of the pipeline parameters file .

NXF_PID_FILE

Name of the file where the process PID is saved when Nextflow is launched in background.

NXF_PLUGINS_ALLOWED

New in version 25.04.0.

Comma separated list of plugin IDs that can be used in a workflow executions e.g. NXF_PLUGINS_ALLOWED=nf-amazon,nf-tower,nf-wave. Use empty string to disallow all plugins.

NXF_PLUGINS_DEFAULT

Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default: true).

NXF_PLUGINS_DIR

The path where the plugin archives are loaded and stored (default: $NXF_HOME/plugins).

NXF_PLUGINS_REGISTRY_URL

New in version 25.08.0-edge.

Specifies the URL of the plugin registry used to download and resolve plugins. This allows using custom or private plugin registries instead of the default public registry.

NXF_PLUGINS_TEST_REPOSITORY

New in version 23.04.0.

Defines a custom plugin registry or plugin release URL for testing plugins outside of the main registry.

NXF_PUBLISH_FAIL_ON_ERROR

New in version 24.04.3.

Defines the default behavior of publishDir.failOnError setting. See publishDir directive for more information.

NXF_RETRY_POLICY_DELAY

New in version 25.06.0-edge.

Delay used for HTTP retryable operations (default: 350ms).

NXF_RETRY_POLICY_JITTER

New in version 25.06.0-edge.

Jitter value used for HTTP retryable operations (default: 0.25).

NXF_RETRY_POLICY_MAX_ATTEMPTS

New in version 25.06.0-edge.

Max number of attempts used for HTTP retryable operations (default: 5).

NXF_RETRY_POLICY_MAX_DELAY

New in version 25.06.0-edge.

Max delay used for HTTP retryable operations (default: 90s).

NXF_RETRY_POLICY_MULTIPLIER

New in version 25.08.0-edge.

Delay multiplier used for HTTP retryable operations (default: 2.0).

NXF_SCM_FILE

New in version 20.10.0.

Defines the path location of the SCM config file .

NXF_SINGULARITY_CACHEDIR

Directory where remote Singularity images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.

NXF_SINGULARITY_LIBRARYDIR

New in version 21.09.0-edge.

Directory where remote Singularity images are retrieved. It should be a directory accessible to all compute nodes.

NXF_SPACK_CACHEDIR

Directory where Spack environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.

NXF_SPACK_ENABLED

New in version 23.02.0-edge.

Enable the use of Spack recipes defined by using the spack directive. (default: false).

NXF_SYNTAX_PARSER

New in version 25.02.0-edge.

Set to 'v2' to use the strict syntax for Nextflow scripts and config files (default: 'v1').

NXF_TEMP

Directory where temporary files are stored

NXF_TRACE

Enable trace level logging for the specified packages. Equivalent to the -trace command-line option.

NXF_VER

Defines which version of Nextflow to use.

NXF_WORK

Directory where working files are stored (usually your scratch directory)

NXF_WRAPPER_STAGE_FILE_THRESHOLD

New in version 23.05.0-edge.

Defines the minimum size of the .command.run staging script for it to be written to a separate .command.stage file (default: '1 MB').

This setting is useful for executors that impose a size limit on job scripts.

Seqera Platform settings

TOWER_ACCESS_TOKEN

Specifies the access token for authenticating with Seqera Platform. Can also be configured using the tower.accessToken config option.

TOWER_API_ENDPOINT

Specifies the Seqera Platform API endpoint (default: https://api.cloud.seqera.io). Can also be configured using the tower.endpoint config option.

TOWER_AUTH_DOMAIN

New in version 25.10.0.

Specifies the Auth0 domain for authenticating with Seqera Platform when connecting to a custom endpoint. When specified, this value takes precedence over the built-in mappings for known Seqera endpoints. Must be used in conjunction with TOWER_AUTH_CLIENT_ID.

TOWER_AUTH_CLIENT_ID

New in version 25.10.0.

Specifies the Auth0 client ID for authenticating with a custom Seqera Platform endpoint. Must be used in conjunction with TOWER_AUTH_DOMAIN.

TOWER_REFRESH_TOKEN

Specifies the refresh token for maintaining authentication with Seqera Platform. Can also be configured using the tower.refreshToken config option.

TOWER_WORKSPACE_ID

Specifies the Seqera Platform workspace ID. Can also be configured using the tower.workspaceId config option.

Other settings

FTP_PROXY

New in version 21.06.0-edge.

Defines the FTP proxy server. Proxy authentication is supported by providing the credentials in the proxy URL, e.g. ftp://user:password@proxy-host.com:port.

HTTP_PROXY

Defines the HTTP proxy server.

New in version 21.06.0-edge: Proxy authentication is supported by providing the credentials in the proxy URL, e.g. http://user:password@proxy-host.com:port.

HTTPS_PROXY

Defines the HTTPS proxy server.

New in version 21.06.0-edge: Proxy authentication is supported by providing the credentials in the proxy URL, e.g. https://user:password@proxy-host.com:port.

NO_COLOR

Disables ANSI color codes in Nextflow log output. When this variable is set, Nextflow prints plain text logs following the NO_COLOR standard.

If both NO_COLOR and NXF_ANSI_LOG are set, NXF_ANSI_LOG takes precedence.

NO_PROXY

Defines one or more host names that should not use the proxy server. Separate multiple names using a comma character.

TERMINAL_WIDTH

Forces the terminal width of ANSI-formatted log output. Overrides automatic terminal width detection and uses the specified width for line wrapping when set to an integer value.