| title | Environment variables |
|---|---|
| description | Reference for all environment variables that control the Nextflow runtime and JVM. |
The following environment variables control the configuration of the Nextflow runtime and the underlying Java virtual machine.
Defines the path location of the Java binary command used to launch Nextflow.
Defines the path location of the Java VM installation used to run Nextflow.
When true, enables agent output mode. In this mode, Nextflow replaces the interactive ANSI log with minimal, structured output optimized for AI agents and non-interactive environments.
The output uses tagged lines such as [PIPELINE], [PROCESS], [WARN], [ERROR], and [SUCCESS]/[FAILED] written to standard output (default: false).
Enables/disables ANSI console output (default true when ANSI terminal is detected).
Enables/disables ANSI completion summary: true\|false (default: print summary if execution last more than 1 minute).
Defines the directory where downloaded pipeline repositories are stored (default: $NXF_HOME/assets)
Defines the base cache directory when using the default cache store (default: "$launchDir/.nextflow").
Directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
Defines the base cache path when using the cloud cache store.
Defines the default cloud driver to be used if not specified in the config file or as command line option, either aws or google.
Directory where Conda environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
Enable the use of Conda recipes defined by using the conda directive. (default: false).
When true, override the container entrypoint with /bin/bash (default: false).
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).
Defines the DSL version that should be used in not specified otherwise in the script of config file (default: 2)
Nextflow automatically checks for a newer version of itself unless this option is enabled (default: false).
Disables the cancellation of child jobs on workflow execution termination.
Disables the automatic type detection of command line parameters.
Disables the requirement for Wave service when enabling the Fusion file system.
Enable to use of AWS SES native API for sending emails in place of legacy SMTP settings (default: false)
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)
Enable Nextflow secrets features (default: true)
Enable Nextflow strict execution mode (default: false)
Enable the use of virtual threads in the Nextflow runtime (default: false)
Defines the default process executor, e.g. sge
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.
When set to true, collect task resource metrics (CPU, memory, I/O) from the Fusion trace file (.fusion/trace.json) produced in the task work directory, replacing the metrics collected by the default bash command-trace wrapper. Requires Fusion to be enabled. GPU metrics from Fusion are always collected regardless of this setting (default: false).
Nextflow home directory (default: $HOME/.nextflow).
Defines the path location of the Java VM installation used to run Nextflow. This variable overrides the JAVA_HOME variable if defined.
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.
The filename of the Nextflow log (default: .nextflow.log).
When true prevents Nextflow from automatically downloading and updating remote project repositories (default: false).
Provides extra options for the Java and Nextflow runtime. It must be a blank separated list of -Dkey[=value] properties.
Default organization prefix when looking for a hosted repository (default: nextflow-io).
Defines the path location of the pipeline parameters file .
Name of the file where the process PID is saved when Nextflow is launched in background.
Comma separated list of plugin IDs that can be used in a workflow executions e.g. NXF_PLUGINS_ALLOWED=nf-amazon,nf-seqera,nf-wave. Use empty string to disallow all plugins.
Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default: true).
The path where the plugin archives are loaded and stored (default: $NXF_HOME/plugins).
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.
Controls how Nextflow reacts when the plugins directory (NXF_PLUGINS_DIR) or a cached plugin directory is not a trusted location — i.e. it is owned by another user or writable by group or others. Such a directory could be modified by other users, allowing untrusted plugin code to run in your Nextflow process. Allowed values are warn (default, logs a warning and continues), strict (aborts the run) and off (disables the check). The check is skipped on filesystems that do not support POSIX permissions.
Defines a custom plugin registry or plugin release URL for testing plugins outside of the main registry.
Defines the default behavior of publishDir.failOnError setting. See publishDir directive for more information.
Delay used for HTTP retryable operations (default: 350ms).
Jitter value used for HTTP retryable operations (default: 0.25).
Max number of attempts used for HTTP retryable operations (default: 5).
Max delay used for HTTP retryable operations (default: 90s).
Delay multiplier used for HTTP retryable operations (default: 2.0).
Defines the path location of the SCM config file .
Directory where remote Singularity images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
Directory where remote Singularity images are retrieved. It should be a directory accessible to all compute nodes.
Directory where Spack environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
Enable the use of Spack recipes defined by using the spack directive. (default: false).
Set to 'v2' to use the strict syntax parser for Nextflow code. Set to 'v1' to fall back to the legacy parser.
Directory where temporary files are stored
Enable trace level logging for the specified packages. Equivalent to the -trace command-line option.
Defines which version of Nextflow to use.
Directory where working files are stored (usually your scratch directory)
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.
The access token for authenticating with Seqera Platform. Can also be configured using the tower.accessToken config option.
The Seqera Platform API endpoint (default: https://api.cloud.seqera.io). Can also be configured using the tower.endpoint config option.
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.
The Auth0 client ID for authenticating with a custom Seqera Platform endpoint. Must be used in conjunction with TOWER_AUTH_DOMAIN.
The refresh token for maintaining authentication with Seqera Platform. Can also be configured using the tower.refreshToken config option.
Specifies the Seqera Platform compute environment ID.
When specified, the scheduler resolves the compute environment directly by this ID instead of inferring a suitable compute environment.
Can also be configured using the tower.computeEnvId config option.
The Seqera Platform workspace ID. Can also be configured using the tower.workspaceId config option.
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.
Defines the HTTP proxy server.
Defines the HTTPS proxy server.
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.
Defines one or more host names that should not use the proxy server. Separate multiple names using a comma character.
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.