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_AGENT_MODE
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).
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: $NXF_HOME/assets)
NXF_CACHE_DIR
Defines the base cache directory when using the default cache store (default: "$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
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
Enable the use of Conda recipes defined by using the conda directive. (default: false).
NXF_CONTAINER_ENTRYPOINT_OVERRIDE
When true, override the container entrypoint with /bin/bash (default: false).
NXF_DATE_FORMAT
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
Defines the DSL version that should be used in not specified otherwise in the script of config file (default: 2)
NXF_DISABLE_CHECK_LATEST
Nextflow automatically checks for a newer version of itself unless this option is enabled (default: false).
NXF_DISABLE_JOBS_CANCELLATION
Disables the cancellation of child jobs on workflow execution termination.
NXF_DISABLE_PARAMS_TYPE_DETECTION
Disables the automatic type detection of command line parameters.
NXF_DISABLE_WAVE_SERVICE
Disables the requirement for Wave service when enabling the Fusion file system.
NXF_ENABLE_AWS_SES
Enable to use of AWS SES native API for sending emails in place of legacy SMTP settings (default: false)
NXF_ENABLE_FS_SYNC
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
Enable Nextflow secrets features (default: true)
NXF_ENABLE_STRICT
Enable Nextflow strict execution mode (default: false)
NXF_ENABLE_VIRTUAL_THREADS
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
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_FUSION_TRACE
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).
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
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).
This option also disables the automatic version check (see NXF_DISABLE_CHECK_LATEST).
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
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.
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
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
Defines a custom plugin registry or plugin release URL for testing plugins outside of the main registry.
NXF_PUBLISH_FAIL_ON_ERROR
Defines the default behavior of publishDir.failOnError setting. See publishDir directive for more information.
NXF_RETRY_POLICY_DELAY
Delay used for HTTP retryable operations (default: 350ms).
NXF_RETRY_POLICY_JITTER
Jitter value used for HTTP retryable operations (default: 0.25).
NXF_RETRY_POLICY_MAX_ATTEMPTS
Max number of attempts used for HTTP retryable operations (default: 5).
NXF_RETRY_POLICY_MAX_DELAY
Max delay used for HTTP retryable operations (default: 90s).
NXF_RETRY_POLICY_MULTIPLIER
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
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
Enable the use of Spack recipes defined by using the spack directive. (default: false).
NXF_SYNTAX_PARSER
The strict parser is disabled by default.
The strict parser is enabled by default.
Set to 'v2' to use the strict syntax parser for Nextflow code. Set to 'v1' to fall back to the legacy parser.
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
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
The access token for authenticating with Seqera Platform. Can also be configured using the tower.accessToken config option.
TOWER_API_ENDPOINT
The Seqera Platform API endpoint (default: https://api.cloud.seqera.io). Can also be configured using the tower.endpoint config option.
TOWER_AUTH_DOMAIN
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
The Auth0 client ID for authenticating with a custom Seqera Platform endpoint. Must be used in conjunction with TOWER_AUTH_DOMAIN.
TOWER_REFRESH_TOKEN
The refresh token for maintaining authentication with Seqera Platform. Can also be configured using the tower.refreshToken config option.
TOWER_COMPUTE_ENV_ID
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.
TOWER_WORKSPACE_ID
The Seqera Platform workspace ID. Can also be configured using the tower.workspaceId config option.
Other settings
FTP_PROXY
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.
HTTPS_PROXY
Defines the HTTPS proxy server.
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.