(config-env-vars)=
The following environment variables control the configuration of the Nextflow runtime and the underlying Java virtual machine.
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.
(nxf-env-vars)=
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: $NXF_HOME/assets)
NXF_CACHE_DIR
: :::{versionadded} 24.02.0-edge
:::
: Defines the base cache directory when using the default cache store (default: "$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
: :::{versionadded} 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
: :::{versionadded} 22.08.0-edge
:::
: Enable the use of Conda recipes defined by using the {ref}process-conda directive. (default: false).
NXF_DEFAULT_DSL
: :::{versionadded} 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
: :::{versionadded} 23.09.0-edge
:::
: Nextflow automatically checks for a newer version of itself unless this option is enabled (default: false).
NXF_DISABLE_JOBS_CANCELLATION
: :::{versionadded} 21.12.0-edge
:::
: Disables the cancellation of child jobs on workflow execution termination.
NXF_DISABLE_PARAMS_TYPE_DETECTION
: :::{versionadded} 23.07.0-edge
:::
: Disables the automatic type detection of command line parameters.
NXF_DISABLE_WAVE_SERVICE
: :::{versionadded} 23.08.0-edge
:::
: Disables the requirement for Wave service when enabling the Fusion file system.
NXF_ENABLE_AWS_SES
: :::{versionadded} 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
: :::{versionadded} 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
: :::{versionadded} 21.09.0-edge
:::
: Enable Nextflow secrets features (default: true)
NXF_ENABLE_STRICT
: :::{versionadded} 22.05.0-edge
:::
: Enable Nextflow strict execution mode (default: false)
NXF_ENABLE_VIRTUAL_THREADS
: :::{versionadded} 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
: :::{versionadded} 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('foo') will be resolved to the absolute path /some/root/path/foo. 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
: :::{versionadded} 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).
: :::{versionchanged} 23.09.0-edge
This option also disables the automatic version check (see NXF_DISABLE_CHECK_LATEST).
:::
: :::{versionchanged} 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
: :::{versionadded} 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_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_TEST_REPOSITORY
: :::{versionadded} 23.04.0
:::
: Defines a custom plugin registry or plugin release URL for testing plugins outside of the main registry. See {ref}testing-plugins for more information.
NXF_PUBLISH_FAIL_ON_ERROR
: :::{versionadded} 24.04.3
:::
: Defines the default behavior of publishDir.failOnError setting. See {ref}publishDir<process-publishdir> directive for more information.
NXF_SCM_FILE
: :::{versionadded} 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
: :::{versionadded} 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
: :::{versionadded} 23.02.0-edge
:::
: Enable the use of Spack recipes defined by using the {ref}process-spack directive. (default: false).
NXF_SYNTAX_PARSER
: :::{versionadded} 25.02.0-edge
:::
: Set to 'v2' to use the {ref}strict syntax <updating-syntax-page> for Nextflow 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
: :::{versionadded} 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.
FTP_PROXY
: :::{versionadded} 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.
: :::{versionadded} 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.
: :::{versionadded} 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_PROXY
: Defines one or more host names that should not use the proxy server. Separate multiple names using a comma character.