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: 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 25.10.0.; 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 25.10.0.; Delay used for HTTP retryable operations (default: 350ms).
NXF_RETRY_POLICY_JITTER: New in version 25.10.0.; Jitter value used for HTTP retryable operations (default: 0.25).
NXF_RETRY_POLICY_MAX_ATTEMPTS: New in version 25.10.0.; Max number of attempts used for HTTP retryable operations (default: 5).
NXF_RETRY_POLICY_MAX_DELAY: New in version 25.10.0.; Max delay used for HTTP retryable operations (default: 90s).
NXF_RETRY_POLICY_MULTIPLIER: New in version 25.10.0.; Delay multiplier used for HTTP retryable operations (default: 2.0).
NXF_SCM_FILE: 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.; Enables writing large staging scripts to a separate .command.stage file. The value defines the minimum size of the .command.run staging script for it to be written to the separate file (default when enabled: '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.