Configuration options

This page lists all of the available settings in the Nextflow configuration.

Unscoped options

The following settings are available:

bucketDir: The remote work directory used by hybrid workflows. Equivalent to the -bucket-dir option of the run command.
cleanup: Delete all files associated with a run in the work directory when the run completes successfully (default: false).; Warning

This option will prevent the use of the resume feature on subsequent executions of that pipeline run.

Warning

This option is not supported for remote work directories, such as Amazon S3, Google Cloud Storage, and Azure Blob Storage.
outputDir: New in version 24.10.0.; The pipeline output directory. Equivalent to the -output-dir option of the run command.
resume: Enable the use of previously cached task executions. Equivalent to the -resume option of the run command.
workDir: The pipeline work directory. Equivalent to the -work-dir option of the run command.

`apptainer`

The apptainer scope controls how Apptainer containers are executed by Nextflow.

The following settings are available:

apptainer.autoMounts: Automatically mount host paths in the executed container (default: true). It requires the user bind control feature to be enabled in your Apptainer installation.
apptainer.cacheDir: The directory where remote Apptainer images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
apptainer.enabled: Execute tasks with Apptainer containers (default: false).
apptainer.engineOptions: Specify additional options supported by the Apptainer engine i.e. apptainer [OPTIONS].
apptainer.envWhitelist: Comma separated list of environment variable names to be included in the container environment.
apptainer.libraryDir: Directory where remote Apptainer images are retrieved. When using a computing cluster it must be a shared folder accessible to all compute nodes.
apptainer.noHttps: Pull the Apptainer image with http protocol (default: false).
apptainer.ociAutoPull: New in version 23.12.0-edge.; When enabled, OCI (and Docker) container images are pulled and converted to the SIF format by the Apptainer run command, instead of Nextflow (default: false).

Note

Leave ociAutoPull disabled if you are willing to build a Singularity/Apptainer native image with Wave (see the Build Singularity native images section).
apptainer.pullTimeout: The amount of time the Apptainer pull can last, exceeding which the process is terminated (default: 20 min).
apptainer.registry: The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. http://.
apptainer.runOptions: Specify extra command line options supported by apptainer exec.

`aws`

The aws scope controls the interactions with AWS, including AWS Batch and S3.

The following settings are available:

aws.accessKey: AWS account access key.
aws.profile: New in version 22.12.0-edge.; AWS profile from ~/.aws/credentials.
aws.region: AWS region (e.g. us-east-1).
aws.secretKey: AWS account secret key.
aws.batch.cliPath: The path where the AWS command line tool is installed in the host AMI.
aws.batch.delayBetweenAttempts: Delay between download attempts from S3 (default: 10 sec).
aws.batch.executionRole: The AWS Batch Execution Role ARN that needs to be used to execute the Batch Job. It is mandatory when using AWS Fargate.
aws.batch.jobRole: The AWS Batch Job Role ARN that needs to be used to execute the Batch Job.
aws.batch.logsGroup: New in version 22.09.0-edge.; The name of the logs group used by Batch Jobs (default: /aws/batch/job).
aws.batch.maxParallelTransfers: Max parallel upload/download transfer operations per job (default: 4).
aws.batch.maxSpotAttempts: New in version 22.04.0.; Changed in version 24.08.0-edge: The default value was changed from 5 to 0.; Max number of execution attempts of a job interrupted by a EC2 Spot reclaim event (default: 0)
aws.batch.maxTransferAttempts: Max number of downloads attempts from S3 (default: 1).
aws.batch.platformType: The compute platform type used by AWS Batch. Can be either ec2 or fargate. Set to fargate to use AWS Fargate.
aws.batch.retryMode: The retry mode used to handle rate-limiting by AWS APIs. Can be one of standard, legacy, adaptive, or built-in (default: standard).
aws.batch.schedulingPriority: New in version 23.01.0-edge.; The scheduling priority for all tasks when using fair-share scheduling (default: 0).
aws.batch.shareIdentifier: New in version 22.09.0-edge.; The share identifier for all tasks when using fair-share scheduling.
aws.batch.terminateUnschedulableJobs: New in version 25.03.0-edge.; When true, jobs that cannot be scheduled due to lack of resources or misconfiguration are terminated and handled as task failures (default: false).
aws.batch.volumes: List of container mounts. Mounts can be specified as simple e.g. /some/path or canonical format e.g. /host/path:/mount/path[:ro|rw].
aws.client.anonymous: Allow the access of public S3 buckets without providing AWS credentials (default: false). Any service that does not accept unsigned requests will return a service access error.
aws.client.connectionTimeout: The amount of time to wait (in milliseconds) when initially establishing a connection before timing out (default: 10000).
aws.client.endpoint: The AWS S3 API entry point e.g. https://s3-us-west-1.amazonaws.com. The endpoint must include the protocol prefix e.g. https://.
aws.client.maxConcurrency: New in version 25.06.0-edge.; The maximum number of concurrent S3 transfers used by the S3 transfer manager. By default, this setting is determined by aws.client.targetThroughputInGbps. Modifying this value can affect the amount of memory used for S3 transfers.
aws.client.maxConnections: The maximum number of open HTTP connections used by the S3 transfer manager (default: 50).
aws.client.maxErrorRetry: The maximum number of retry attempts for failed retryable requests (default: -1).
aws.client.maxNativeMemory: New in version 25.06.0-edge.; The maximum native memory used by the S3 transfer manager. By default, this setting is determined by aws.client.targetThroughputInGbps.
aws.client.minimumPartSize: New in version 25.06.0-edge.; The minimum part size used by the S3 transfer manager for multi-part uploads (default: 8 MB).
aws.client.multipartThreshold: New in version 25.06.0-edge.; The object size threshold used by the S3 transfer manager for performing multi-part uploads (default: same as aws.cllient.minimumPartSize).
aws.client.protocol: Deprecated since version 25.06.0-edge: This option is no longer supported.; The protocol to use when connecting to AWS. Can be http or https (default: 'https').
aws.client.proxyHost: The proxy host to connect through.
aws.client.proxyPassword: The password to use when connecting through a proxy.
aws.client.proxyPort: The port to use when connecting through a proxy.
aws.client.proxyScheme: New in version 25.06.0-edge.; The protocol scheme to use when connecting through a proxy. Can be http or https (default: 'http').
aws.client.proxyUsername: The user name to use when connecting through a proxy.
aws.client.requesterPays: New in version 24.05.0-edge.; Use Requester Pays for S3 buckets (default: false).
aws.client.s3Acl: Specify predefined bucket permissions, also known as canned ACL. Can be one of Private, PublicRead, PublicReadWrite, AuthenticatedRead, LogDeliveryWrite, BucketOwnerRead, BucketOwnerFullControl, or AwsExecRead.
aws.client.s3PathStyleAccess: Use the path-based access model to access objects in S3-compatible storage systems (default: false).
aws.client.signerOverride: Deprecated since version 25.06.0-edge: This option is no longer supported.; The name of the signature algorithm to use for signing requests made by the client.
aws.client.socketSendBufferSizeHint: Deprecated since version 25.06.0-edge: This option is no longer supported.; The Size hint (in bytes) for the low level TCP send buffer (default: 0).
aws.client.socketRecvBufferSizeHint: Deprecated since version 25.06.0-edge: This option is no longer supported.; The Size hint (in bytes) for the low level TCP receive buffer (default: 0).
aws.client.socketTimeout: The amount of time to wait (in milliseconds) for data to be transferred over an established, open connection before the connection is timed out (default: 50000).
aws.client.storageClass: The S3 storage class applied to stored objects, one of [STANDARD, STANDARD_IA, ONEZONE_IA, INTELLIGENT_TIERING] (default: STANDARD).
aws.client.storageEncryption: The S3 server side encryption to be used when saving objects on S3. Can be AES256 or aws:kms (default: none).
aws.client.storageKmsKeyId: New in version 22.05.0-edge.; The AWS KMS key Id to be used to encrypt files stored in the target S3 bucket.
aws.client.targetThroughputInGbps: New in version 25.06.0-edge.; The target network throughput (in Gbps) used by the S3 transfer manager (default: 10). This setting is not used when aws.client.maxConcurrency and aws.client.maxNativeMemory are specified.
aws.client.transferManagerThreads: New in version 25.06.0-edge.; The number of threads used by the S3 transfer manager (default: 10).
aws.client.userAgent: Deprecated since version 25.06.0-edge: This option is no longer supported.; The HTTP user agent header passed with all HTTP requests.
aws.client.uploadChunkSize: Deprecated since version 25.06.0-edge: This option is no longer supported.; The size of a single part in a multipart upload (default: 100 MB).
aws.client.uploadMaxAttempts: Deprecated since version 25.06.0-edge: This option is no longer supported.; The maximum number of upload attempts after which a multipart upload returns an error (default: 5).
aws.client.uploadMaxThreads: Deprecated since version 25.06.0-edge: This option is no longer supported.; The maximum number of threads used for multipart upload (default: 10).
aws.client.uploadRetrySleep: Deprecated since version 25.06.0-edge: This option is no longer supported.; The time to wait after a failed upload attempt to retry the part upload (default: 500ms).
aws.client.uploadStorageClass: The S3 storage class applied to stored objects. Can be STANDARD, STANDARD_IA, ONEZONE_IA, or INTELLIGENT_TIERING (default: STANDARD).

`azure`

The azure scope allows you to configure the interactions with Azure, including Azure Batch and Azure Blob Storage.

The following settings are available:

azure.activeDirectory.servicePrincipalId

The service principal client ID. Defaults to environment variable AZURE_CLIENT_ID.

azure.activeDirectory.servicePrincipalSecret

The service principal client secret. Defaults to environment variable AZURE_CLIENT_SECRET.

azure.activeDirectory.tenantId

The Azure tenant ID. Defaults to environment variable AZURE_TENANT_ID.

azure.azcopy.blobTier

The blob access tier used by azcopy to upload files to Azure Blob Storage. Valid options are None, Hot, or Cool (default: None).

azure.azcopy.blockSize

The block size (in MB) used by azcopy to transfer files between Azure Blob Storage and compute nodes (default: 4).

azure.batch.accountKey

The batch service account key. Defaults to environment variable AZURE_BATCH_ACCOUNT_KEY.

azure.batch.accountName

The batch service account name. Defaults to environment variable AZURE_BATCH_ACCOUNT_NAME.

azure.batch.allowPoolCreation

Enable the automatic creation of batch pools specified in the Nextflow configuration file (default: false).

azure.batch.autoPoolMode

Enable the automatic creation of batch pools depending on the pipeline resources demand (default: true).

azure.batch.copyToolInstallMode

The mode in which the azcopy tool is installed by Nextflow (default: 'node').

The following options are available:

'node': The azcopy tool is installed once during the pool creation.
'task': The azcopy tool is installed for each task execution.
'off': The azcopy tool is not installed.

azure.batch.deleteJobsOnCompletion

Changed in version 23.08.0-edge: Default value was changed from true to false.

Delete all jobs when the workflow completes (default: false).

azure.batch.deletePoolsOnCompletion

Delete all compute node pools when the workflow completes (default: false).

azure.batch.deleteTasksOnCompletion

New in version 23.08.0-edge.

Delete each task when it completes (default: true).

Although this setting is enabled by default, failed tasks will not be deleted unless it is explicitly enabled. This way, the default behavior is that successful tasks are deleted while failed tasks are preserved for debugging purposes.

azure.batch.endpoint

The batch service endpoint e.g. https://nfbatch1.westeurope.batch.azure.com.

azure.batch.jobMaxWallClockTime

New in version 25.04.0.

The maximum elapsed time that jobs may run, measured from the time they are created (default: 30d).

If jobs do not complete within this time limit, the Batch service terminates them and any tasks still running.

azure.batch.location

The name of the batch service region, e.g. westeurope or eastus2. Not needed when the endpoint is specified.

azure.batch.poolIdentityClientId

New in version 25.05.0-edge.

The client ID for an Azure managed identity that is available on all Azure Batch node pools. This identity is used by Fusion to authenticate to Azure storage. If set to 'auto', Fusion will use the first available managed identity.

azure.batch.pools.<name>.autoScale

Enable autoscaling feature for the pool identified with <name>.

azure.batch.pools.<name>.fileShareRootPath

The internal root mount point when mounting File Shares. Must be /mnt/resource/batch/tasks/fsmounts for CentOS nodes or /mnt/batch/tasks/fsmounts for Ubuntu nodes (default: CentOS).

azure.batch.pools.<name>.lowPriority

Enable the use of low-priority VMs (default: false).

Warning

As of September 30, 2025, Low Priority VMs will no longer be supported in Azure Batch accounts that use Batch Managed mode for pool allocation. You may continue to use this setting to configure Spot VMs in Batch accounts configured with User Subscription mode.

azure.batch.pools.<name>.maxVmCount

The max number of virtual machines when using auto scaling.

azure.batch.pools.<name>.mountOptions

The mount options for mounting the file shares (default: -o vers=3.0,dir_mode=0777,file_mode=0777,sec=ntlmssp).

azure.batch.pools.<name>.offer

The offer type of the virtual machine type used by the pool identified with <name> (default: centos-container).

azure.batch.pools.<name>.privileged

Enable the task to run with elevated access. Ignored if runAs is set (default: false).

azure.batch.pools.<name>.publisher

The publisher of virtual machine type used by the pool identified with <name> (default: microsoft-azure-batch).

azure.batch.pools.<name>.runAs

The username under which the task is run. The user must already exist on each node of the pool.

azure.batch.pools.<name>.scaleFormula

The scale formula for the pool identified with <name>.

azure.batch.pools.<name>.scaleInterval

The interval at which to automatically adjust the Pool size according to the autoscale formula. Must be at least 5 minutes and at most 168 hours (default: 10 mins).

azure.batch.pools.<name>.schedulePolicy

The scheduling policy for the pool identified with <name>. Can be either spread or pack (default: spread).

azure.batch.pools.<name>.sku

The ID of the Compute Node agent SKU which the pool identified with <name> supports (default: batch.node.centos 8).

azure.batch.pools.<name>.startTask.privileged

New in version 24.03.0-edge.

Enable the startTask to run with elevated access (default: false).

azure.batch.pools.<name>.startTask.script

New in version 24.03.0-edge.

The startTask that is executed as the node joins the Azure Batch node pool.

azure.batch.pools.<name>.virtualNetwork

New in version 23.03.0-edge.

The subnet ID of a virtual network in which to create the pool.

azure.batch.pools.<name>.vmCount

The number of virtual machines provisioned by the pool identified with <name>.

azure.batch.pools.<name>.vmType

The virtual machine type used by the pool identified with <name>.

azure.batch.terminateJobsOnCompletion

New in version 23.05.0-edge.

When the workflow completes, set all jobs to terminate on task completion (default: true).

azure.managedIdentity.clientId

The client ID for an Azure managed identity. Defaults to environment variable AZURE_MANAGED_IDENTITY_USER.

azure.managedIdentity.system

When true, use the system-assigned managed identity to authenticate Azure resources. Defaults to environment variable AZURE_MANAGED_IDENTITY_SYSTEM.

azure.registry.password

The password to connect to a private container registry.

azure.registry.server

The container registry from which to pull the Docker images (default: docker.io).

azure.registry.userName

The username to connect to a private container registry.

azure.retryPolicy.delay

Delay when retrying failed API requests (default: 250ms).

azure.retryPolicy.jitter

Jitter value when retrying failed API requests (default: 0.25).

azure.retryPolicy.maxAttempts

Max attempts when retrying failed API requests (default: 10).

azure.retryPolicy.maxDelay

Max delay when retrying failed API requests (default: 90s).

azure.storage.accountKey

The blob storage account key. Defaults to environment variable AZURE_STORAGE_ACCOUNT_KEY.

azure.storage.accountName

The blob storage account name. Defaults to environment variable AZURE_STORAGE_ACCOUNT_NAME.

azure.storage.fileShares.<name>.mountOptions

The file share mount options.

azure.storage.fileShares.<name>.mountPath

The file share mount path.

azure.storage.sasToken

The blob storage shared access signature (SAS) token, which can be provided instead of an account key. Defaults to environment variable AZURE_STORAGE_SAS_TOKEN.

azure.storage.tokenDuration

The duration of the SAS token generated by Nextflow when the sasToken option is not specified (default: 48h).

`charliecloud`

The charliecloud scope controls how Charliecloud containers are executed by Nextflow.

The following settings are available:

charliecloud.cacheDir: The directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
charliecloud.enabled: Execute tasks with Charliecloud containers (default: false).
charliecloud.envWhitelist: Comma separated list of environment variable names to be included in the container environment.
charliecloud.pullTimeout: The amount of time the Charliecloud pull can last, exceeding which the process is terminated (default: 20 min).
charliecloud.registry: The registry from where images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. http://.
charliecloud.runOptions: Specify extra command line options supported by the ch-run command.
charliecloud.temp: Mounts a path of your choice as the /tmp directory in the container. Use the special value 'auto' to create a temporary directory each time a container is created.
charliecloud.writableInputMounts: When false, mount input directories as read-only (default: true).
charliecloud.writeFake: Run containers from storage in writeable mode using overlayfs (default: true).; This option requires unprivileged overlayfs (Linux kernel >= 5.11). For full support, tempfs with xattrs in the user namespace (Linux kernel >= 6.6) is required. See charliecloud documentation for details.

`conda`

The conda scope controls the creation of Conda environments by the Conda package manager.

The following settings are available:

conda.cacheDir: The path where Conda environments are stored. It should be accessible from all compute nodes when using a shared file system.
conda.channels: The list of Conda channels that can be used to resolve Conda packages. Channel priority decreases from left to right.
conda.createOptions: Extra command line options for the conda create command. See the Conda documentation for more information.
conda.createTimeout: The amount of time to wait for the Conda environment to be created before failing (default: 20 min).
conda.enabled: Execute tasks with Conda environments (default: false).
conda.useMamba: Use Mamba instead of conda to create Conda environments (default: false).
conda.useMicromamba: New in version 22.05.0-edge.; Use Micromamba instead of conda to create Conda environments (default: false).

`dag`

The dag scope controls the workflow diagram generated by Nextflow.

The following settings are available:

dag.depth: New in version 23.10.0.; Supported by the HTML and Mermaid renderers.; Controls the maximum depth at which to render sub-workflows (default: no limit).
dag.direction: New in version 23.10.0.; Supported by the Graphviz, DOT, HTML and Mermaid renderers.; Controls the direction of the DAG, can be 'LR' (left-to-right) or 'TB' (top-to-bottom) (default: 'TB').
dag.enabled: When true enables the generation of the DAG file (default: false).
dag.file: Graph file name (default: 'dag-<timestamp>.html').
dag.overwrite: When true overwrites any existing DAG file with the same name (default: false).
dag.verbose: New in version 23.10.0.; Only supported by the HTML and Mermaid renderers.; When false, channel names are omitted, operators are collapsed, and empty workflow inputs are removed (default: false).

`docker`

The docker scope controls how Docker containers are executed by Nextflow.

The following settings are available:

docker.enabled: Enable Docker execution (default: false).
docker.engineOptions: Specify additional options supported by the Docker engine i.e. docker [OPTIONS].
docker.envWhitelist: Comma separated list of environment variable names to be included in the container environment.
docker.fixOwnership: Fix ownership of files created by the Docker container (default: false).
docker.legacy: Use command line options removed since Docker 1.10.0 (default: false).
docker.mountFlags: Add the specified flags to the volume mounts e.g. 'ro,Z'.
docker.registry: The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. http://.
docker.registryOverride: New in version 25.06.0-edge.; When true, forces the override of the registry name in fully qualified container image names with the registry specified by docker.registry (default: false).; This setting allows you to redirect container image pulls from their original registry to a different registry, such as a private mirror or proxy.
docker.remove: Clean up the container after the execution (default: true). See the Docker documentation for details.
docker.runOptions: Specify extra command line options supported by the docker run command. See the Docker documentation for details.
docker.sudo: Executes Docker run command as sudo (default: false).
docker.temp: Mounts a path of your choice as the /tmp directory in the container. Use the special value 'auto' to create a temporary directory each time a container is created.
docker.tty: Allocates a pseudo-tty (default: false).
docker.writableInputMounts: When false, mount input directories as read-only (default: true).

`env`

The env scope allows the definition one or more variables that will be exported into the environment where workflow tasks are executed.

Simply prefix your variable names with the env scope or surround them by curly brackets, as shown below:

env.ALPHA = 'some value'
env.BETA = "$HOME/some/path"

env {
     DELTA = 'one more'
     GAMMA = "/my/path:$PATH"
}

Note

In the above example, variables like $HOME and $PATH are evaluated when the workflow is launched. If you want these variables to be evaluated during task execution, escape them with \$. This difference is important for variables like $PATH, which may be different in the workflow environment versus the task environment.

Warning

The env scope provides environment variables to tasks, not Nextflow itself. Nextflow environment variables such as NXF_VER should be set in the environment in which Nextflow is launched.

`executor`

The executor scope controls various executor behaviors.

The following settings are available:

executor.account

New in version 24.04.0.

Used only by the SLURM, LSF, PBS/Torque and PBS Pro executors.

The project or organization account that should be charged for running the pipeline jobs.

executor.cpus

Used only by the local executor.

The maximum number of CPUs made available by the underlying system.

executor.dumpInterval

Determines how often to log the executor status (default: 5 min).

executor.exitReadTimeout

Used only by grid executors.

Determines how long to wait for the .exitcode file to be created after the task has completed, before returning an error status (default: 270 sec).

executor.jobName

Used only by grid executors and Google Batch.

Determines the name of jobs submitted to the underlying cluster executor:

executor.jobName = { "$task.name - $task.hash" }

The job name should satisfy the validation constraints of the underlying scheduler.

executor.killBatchSize

Determines the number of jobs that can be killed in a single command execution (default: 100).

executor.memory

Used only by the local executor.

The maximum amount of memory made available by the underlying system.

executor.name

The name of the executor to be used (default: local).

executor.perCpuMemAllocation

New in version 23.07.0-edge.

Used only by the SLURM executor.

When true, memory allocations for SLURM jobs are specified as --mem-per-cpu <task.memory / task.cpus> instead of --mem <task.memory>.

executor.perJobMemLimit

Used only by the LSF executor.

Enables the per-job memory limit mode for LSF jobs.

executor.perTaskReserve

Used only by the LSF executor.

Enables the per-task memory reserve mode for LSF jobs.

executor.pollInterval

Determines how often to check for process termination. Default varies for each executor.

executor.queueGlobalStatus

New in version 23.01.0-edge.

Determines how job status is retrieved. When false only the queue associated with the job execution is queried. When true the job status is queried globally i.e. irrespective of the submission queue (default: false).

executor.queueSize

The number of tasks the executor will handle in a parallel manner. A queue size of zero corresponds to no limit. Default varies for each executor.

executor.queueStatInterval

Used only by grid executors.

Determines how often to fetch the queue status from the scheduler (default: 1 min).

executor.submitRateLimit

Determines the max rate of job submission per time unit, for example '10sec' (10 jobs per second) or '50/2min' (50 jobs every 2 minutes) (default: unlimited).

executor.retry.delay

New in version 22.03.0-edge.

Used only by grid executors.

Delay when retrying failed job submissions (default: 500ms).

executor.retry.jitter

New in version 22.03.0-edge.

Used only by grid executors.

Jitter value when retrying failed job submissions (default: 0.25).

executor.retry.maxAttempts

New in version 22.03.0-edge.

Used only by grid executors.

Max attempts when retrying failed job submissions (default: 3).

executor.retry.maxDelay

New in version 22.03.0-edge.

Used only by grid executors.

Max delay when retrying failed job submissions (default: 30s).

executor.retry.reason

New in version 22.03.0-edge.

Changed in version 25.10.0: This option was renamed from executor.submit.retry.reason to executor.retry.reason.

Used only by grid executors.

Regex pattern that when verified causes a failed submit operation to be re-tried (default: Socket timed out).

Executor-specific defaults

Some executor settings have different default values depending on the executor.

Executor	`queueSize`	`pollInterval`
AWS Batch	`1000`	`10s`
Azure Batch	`1000`	`10s`
Google Batch	`1000`	`10s`
Grid Executors	`100`	`5s`
Kubernetes	`100`	`5s`
Local	N/A	`100ms`

Executor-specific configuration

Executor config settings can be applied to specific executors by prefixing the executor name with the symbol $ and using it as special scope. For example:

// block syntax
executor {
  $sge {
      queueSize = 100
      pollInterval = '30sec'
  }

  $local {
      cpus = 8
      memory = '32 GB'
  }
}

// dot syntax
executor.$sge.queueSize = 100
executor.$sge.pollInterval = '30sec'
executor.$local.cpus = 8
executor.$local.memory = '32 GB'

`fusion`

The fusion scope provides advanced configuration for the use of the Fusion file system.

The following settings are available:

fusion.cacheSize: New in version 23.11.0-edge.; The maximum size of the local cache used by the Fusion client.
fusion.containerConfigUrl: The URL of the container layer that provides the Fusion client.
fusion.enabled: Enable the Fusion file system (default: false).
fusion.exportStorageCredentials: Export the access credentials required by the underlying object storage to the task execution environment (default: false).
fusion.logLevel: The log level of the Fusion client.
fusion.logOutput: The output location of the Fusion log.
fusion.privileged: New in version 23.10.0.; Enable privileged containers for Fusion (default: true).; Non-privileged use is supported only on Kubernetes with the k8s-fuse-plugin or a similar FUSE device plugin.
fusion.snapshots: New in version 25.03.0-edge.; Currently only supported for AWS Batch; Enable Fusion snapshotting (preview, default: false). This feature allows Fusion to automatically restore a job when it is interrupted by a spot reclamation.
fusion.tags: The pattern that determines how tags are applied to files created via the Fusion client (default: [.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)). Set to false to disable tags.

`google`

The google scope allows you to configure the interactions with Google Cloud, including Google Cloud Batch and Google Cloud Storage.

The following settings are available:

google.enableRequesterPaysBuckets

Use the given Google Cloud project ID as the billing project for storage access (default: false). Required when accessing data from requester pays buckets.

google.httpConnectTimeout

New in version 23.06.0-edge.

The HTTP connection timeout for Cloud Storage API requests (default: '60s').

google.httpReadTimeout

New in version 23.06.0-edge.

The HTTP read timeout for Cloud Storage API requests (default: '60s').

google.location

The Google Cloud location where jobs are executed (default: us-central1).

google.project

The Google Cloud project ID to use for pipeline execution.

google.batch.allowedLocations

New in version 22.12.0-edge.

The set of allowed locations for VMs to be provisioned (default: no restriction).

google.batch.autoRetryExitCodes

New in version 24.07.0-edge.

The list of exit codes that should be automatically retried by Google Batch when google.batch.maxSpotAttempts is greater than 0 (default: [50001]).

See Google Batch documentation for the complete list of retryable exit codes.

google.batch.bootDiskImage

New in version 24.08.0-edge.

The image URI of the virtual machine boot disk, e.g batch-debian (default: none).

See Google documentation for details.

google.batch.bootDiskSize

The size of the virtual machine boot disk, e.g 50.GB (default: none).

google.batch.cpuPlatform

The minimum CPU Platform, e.g. 'Intel Skylake' (default: none).

google.batch.gcsfuseOptions

New in version 25.03.0-edge.

List of custom mount options for gcsfuse (default: ['-o rw', '-implicit-dirs']).

google.batch.maxSpotAttempts

New in version 23.11.0-edge.

Changed in version 24.08.0-edge: The default value was changed from 5 to 0.

Max number of execution attempts of a job interrupted by a Compute Engine Spot reclaim event (default: 0).

See also: google.batch.autoRetryExitCodes

google.batch.network

The URL of an existing network resource to which the VM will be attached.

You can specify the network as a full or partial URL. For example, the following are all valid URLs:

https://www.googleapis.com/compute/v1/projects/{project}/global/networks/{network}
projects/{project}/global/networks/{network}
global/networks/{network}

google.batch.networkTags

The network tags to be applied to the instances created by Google Batch jobs (e.g., ['allow-ssh', 'allow-http']).

Network tags are ignored when using instance templates.

google.batch.serviceAccountEmail

The Google service account email to use for the pipeline execution. If not specified, the default Compute Engine service account for the project will be used.

This service account will only be used for tasks submitted by Nextflow, not for Nextflow itself. See Credentials for more information on Google Cloud credentials.

google.batch.spot

Enable the use of spot virtual machines (default: false).

google.batch.subnetwork

The URL of an existing subnetwork resource in the network to which the VM will be attached.

You can specify the subnetwork as a full or partial URL. For example, the following are all valid URLs:

https://www.googleapis.com/compute/v1/projects/{project}/regions/{region}/subnetworks/{subnetwork}
projects/{project}/regions/{region}/subnetworks/{subnetwork}
regions/{region}/subnetworks/{subnetwork}

google.batch.usePrivateAddress

Do not provision public IP addresses for VMs, such that they only have an internal IP address (default: false).

When this option is enabled, jobs can only load Docker images from Google Container Registry, and cannot use external services other than Google APIs.

google.storage.retryPolicy.maxAttempts

New in version 23.11.0-edge.

Max attempts when retrying failed API requests to Cloud Storage (default: 10).

google.storage.retryPolicy.maxDelay

New in version 23.11.0-edge.

Max delay when retrying failed API requests to Cloud Storage (default: '90s').

google.storage.retryPolicy.multiplier

New in version 23.11.0-edge.

Delay multiplier when retrying failed API requests to Cloud Storage (default: 2.0).

`k8s`

The k8s scope controls the deployment and execution of workflow applications in a Kubernetes cluster.

The following settings are available:

k8s.autoMountHostPaths

Automatically mount host paths into the task pods (default: false). Only intended for development purposes when using a single node.

k8s.cleanup

When true, successful pods are automatically deleted (default: true).

k8s.client

Map of options for the Kubernetes HTTP client.

If this option is specified, it will be used instead of .kube/config.

The following options are available:

server
token
tokenFile
verifySsl
sslCert
sslCertFile
clientCert
clientCertFile
clientKey
clientKeyFile

k8s.computeResourceType

New in version 22.05.0-edge.

Whether to use Kubernetes Pod or Job resource type to carry out Nextflow tasks (default: Pod).

k8s.context

The Kubernetes configuration context to use.

k8s.cpuLimits

New in version 24.04.0.

When true, set both the pod CPUs request and limit to the value specified by the cpus directive, otherwise set only the request (default: false).

This setting is useful when a K8s cluster requires a CPU limit to be defined through a LimitRange.

k8s.fetchNodeName

New in version 22.05.0-edge.

Include the hostname of each task in the execution trace (default: false).

k8s.fuseDevicePlugin

New in version 24.01.0-edge.

The FUSE device plugin to be used when enabling Fusion in unprivileged mode (default: ['nextflow.io/fuse': 1]).

k8s.httpConnectTimeout

New in version 22.10.0.

The Kubernetes HTTP client request connection timeout e.g. '60s'.

k8s.httpReadTimeout

New in version 22.10.0.

The Kubernetes HTTP client request connection read timeout e.g. '60s'.

k8s.imagePullPolicy

The strategy for pulling container images. Can be IfNotPresent, Always, Never.

k8s.launchDir

The path where the workflow is launched and the user data is stored (default: <volume-claim-mount-path>/<user-name>). Must be a path in a shared K8s persistent volume.

k8s.namespace

The Kubernetes namespace to use (default: default).

k8s.pod

Additional pod configuration options such as environment variables, config maps, secrets, etc. Allows the same settings as the pod process directive.

When using the kuberun command, this setting also applies to the submitter pod.

k8s.projectDir

The path where Nextflow projects are downloaded (default: <volume-claim-mount-path>/projects). Must be a path in a shared K8s persistent volume.

k8s.runAsUser

The user ID to be used to run the containers. Shortcut for the securityContext option.

k8s.securityContext

The security context to use for all pods.

k8s.serviceAccount

The Kubernetes service account name to use.

k8s.storageClaimName

The name of the persistent volume claim where the shared work directory is stored.

k8s.storageMountPath

The mount path for the persistent volume claim (default: /workspace).

k8s.storageSubPath

The path in the persistent volume to be mounted (default: /).

k8s.workDir

The path of the shared work directory (default: <user-dir>/work). Must be a path in a shared K8s persistent volume.

k8s.debug.yaml

Save the pod spec for each task to .command.yaml in the task directory (default: false).

k8s.retryPolicy.delay

Delay when retrying failed API requests (default: 250ms).

k8s.retryPolicy.jitter

Jitter value when retrying failed API requests (default: 0.25).

k8s.retryPolicy.maxAttempts

Max attempts when retrying failed API requests (default: 4).

k8s.retryPolicy.maxDelay

Max delay when retrying failed API requests (default: 90s).

`lineage`

The lineage scope controls the generation of lineage metadata.

The following settings are available:

lineage.enabled: Enable generation of lineage metadata (default: false).
lineage.store.location: The location of the lineage metadata store (default: ./.lineage).

`mail`

The mail scope controls the mail server used to send email notifications.

The following settings are available:

mail.debug: Enable Java Mail logging for debugging purposes (default: false).
mail.from: Default email sender address.
mail.smtp.host: Host name of the mail server.
mail.smtp.password: User password to connect to the mail server.
mail.smtp.port: Port number of the mail server.
mail.smtp.user: User name to connect to the mail server.
mail.smtp.proxy.host: Host name of an HTTP web proxy server that will be used for connections to the mail server.
mail.smtp.proxy.port: Port number for the HTTP web proxy server.
mail.smtp.*: Any SMTP configuration property supported by the Java Mail API, which Nextflow uses to send emails. See the table of available properties here.

`manifest`

The manifest scope allows you to define some metadata that is useful when publishing or running your pipeline.

The following settings are available:

manifest.author

Deprecated since version 24.09.0-edge: Use manifest.contributors instead.

Project author name (use a comma to separate multiple names).

manifest.contributors

New in version 24.09.0-edge.

List of project contributors. Should be a list of maps.

The following fields are supported in the contributor map:

name: The contributor name.
affiliation: The contributor affiliated organization.
email: The contributor email address.
github: The contributor GitHub URL.
contribution: List of contribution types, each element can be one of 'author', 'maintainer', or 'contributor'.
orcid: The contributor ORCID URL.

manifest.defaultBranch

Git repository default branch (default: master).

manifest.description

Free text describing the workflow project.

manifest.docsUrl

Project documentation URL.

manifest.doi

Project related publication DOI identifier.

manifest.gitmodules

Controls whether git sub-modules should be cloned with the main repository.

Can be either a boolean value, a list of submodule names, or a comma-separated string of submodule names.

manifest.homePage

Project home page URL.

manifest.icon

Project related icon location (Relative path or URL).

manifest.license

Project license.

manifest.mainScript

Project main script (default: main.nf).

manifest.name

Project short name.

manifest.nextflowVersion

Minimum required Nextflow version.

This setting may be useful to ensure that a specific version is used:

manifest.nextflowVersion = '1.2.3'        // exact match
manifest.nextflowVersion = '1.2+'         // 1.2 or later (excluding 2 and later)
manifest.nextflowVersion = '>=1.2'        // 1.2 or later
manifest.nextflowVersion = '>=1.2, <=1.5' // any version in the 1.2 .. 1.5 range
manifest.nextflowVersion = '!>=1.2'       // with ! prefix, stop execution if current version does not match required version.

See VersionNumber for details.

manifest.organization

Project organization.

manifest.recurseSubmodules

Pull submodules recursively from the Git repository.

manifest.version

Project version number.

`nextflow`

Changed in version 24.10.0: The nextflow.publish.retryPolicy settings were moved to workflow.output.retryPolicy.

Changed in version 25.06.0-edge: The workflow.output.retryPolicy settings were moved to nextflow.retryPolicy.

retryPolicy.delay: Delay used for retryable operations (default: 350ms).
retryPolicy.jitter: Jitter value used for retryable operations (default: 0.25).
retryPolicy.maxAttempts: Max attempts used for retryable operations (default: 5).
retryPolicy.maxDelay: Max delay used for retryable operations (default: 90s).

`notification`

The notification scope controls the automatic sending of an email notification on workflow completion.

The following settings are available:

notification.attributes: Map of variables that can be used in the template file.
notification.enabled: Send an email notification when the workflow execution completes (default: false).
notification.from: Sender address for the email notification.
notification.template: Path of a template file containing the contents of the email notification.
notification.to: Recipient address for the email notification. Multiple addresses can be specified as a comma-separated list.

`podman`

The podman scope controls how Podman containers are executed by Nextflow.

The following settings are available:

podman.enabled: Execute tasks with Podman containers (default: false).
podman.engineOptions: Specify additional options supported by the Podman engine i.e. podman [OPTIONS].
podman.envWhitelist: Comma separated list of environment variable names to be included in the container environment.
podman.mountFlags: Add the specified flags to the volume mounts e.g. 'ro,Z'.
podman.registry: The registry from where container images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. http://.
podman.remove: Clean-up the container after the execution (default: true).
podman.runOptions: Specify extra command line options supported by the podman run command.
podman.temp: Mounts a path of your choice as the /tmp directory in the container. Use the special value 'auto' to create a temporary directory each time a container is created.

`report`

The report scope allows you to configure the workflow Execution report.

The following settings are available:

report.enabled: Create the execution report on workflow completion (default: false).
report.file: The path of the created execution report file (default: 'report-<timestamp>.html').
report.overwrite: Overwrite any existing report file with the same name (default: false).

`sarus`

The sarus scope controls how Sarus containers are executed by Nextflow.

The following settings are available:

sarus.enabled: Execute tasks with Sarus containers (default: false).
sarus.envWhitelist: Comma-separated list of environment variable names to be included in the container environment.
sarus.runOptions: Specify extra command line options supported by the sarus run command.; See the Sarus user guide for details.
sarus.tty: Allocates a pseudo-tty (default: false).

`shifter`

The shifter scope controls how Shifter containers are executed by Nextflow.

The following settings are available:

shifter.enabled: Execute tasks with Shifter containers (default: false).
shifter.envWhitelist: Comma-separated list of environment variable names to be included in the container environment.

`singularity`

The singularity scope controls how Singularity containers are executed by Nextflow.

The following settings are available:

singularity.autoMounts: Changed in version 23.09.0-edge: Default value was changed from false to true.; Automatically mount host paths in the executed container (default: true). It requires the user bind control feature to be enabled in your Singularity installation.
singularity.cacheDir: The directory where remote Singularity images are stored. When using a compute cluster, it must be a shared folder accessible to all compute nodes.
singularity.enabled: Execute tasks with Singularity containers (default: false).
singularity.engineOptions: Specify additional options supported by the Singularity engine i.e. singularity [OPTIONS].
singularity.envWhitelist: Comma separated list of environment variable names to be included in the container environment.
singularity.libraryDir: Directory where remote Singularity images are retrieved. When using a computing cluster it must be a shared folder accessible to all compute nodes.
singularity.noHttps: Pull the Singularity image with http protocol (default: false).
singularity.ociAutoPull: New in version 23.12.0-edge.; Requires Singularity 3.11 or later; When enabled, OCI (and Docker) container images are pull and converted to a SIF image file format implicitly by the Singularity run command, instead of Nextflow (default: false).

Note

Leave ociAutoPull disabled if willing to build a Singularity native image with Wave (see the Build Singularity native images section).
singularity.ociMode: New in version 23.12.0-edge.; Requires Singularity 4 or later; Enable OCI-mode, that allows running native OCI compliant container image with Singularity using crun or runc as low-level runtime (default: false).; See --oci flag in the Singularity documentation for more details and requirements (default: false).

Note

Leave ociMode disabled if you are willing to build a Singularity native image with Wave (see the Build Singularity native images section).
singularity.pullTimeout: The amount of time the Singularity pull can last, after which the process is terminated (default: 20 min).
singularity.registry: New in version 22.12.0-edge.; The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. http://.
singularity.runOptions: Specify extra command line options supported by singularity exec.

`spack`

The spack scope controls the creation of a Spack environment by the Spack package manager.

The following settings are available:

spack.cacheDir: The path where Spack environments are stored. It should be accessible from all compute nodes when using a shared file system.
spack.checksum: Enable checksum verification of source tarballs (default: true).; Only disable when requesting a package version not yet encoded in the corresponding Spack recipe.
spack.createTimeout: The amount of time to wait for the Spack environment to be created before failing (default: 60 min).
spack.enabled: Execute tasks with Spack environments (default: false).
spack.parallelBuilds: The maximum number of parallel package builds (default: the number of available CPUs).

`timeline`

The timeline scope controls the execution timeline report generated by Nextflow.

The following settings are available:

timeline.enabled: Create the timeline report on workflow completion file (default: false).
timeline.file: Timeline file name (default: 'timeline-<timestamp>.html').
timeline.overwrite: Overwrite any existing timeline file with the same name (default: false).

`tower`

The tower scope controls the settings for Seqera Platform (formerly Tower Cloud).

The following settings are available:

tower.accessToken: The unique access token for your Seqera Platform account.; Your accessToken can be obtained from your Seqera Platform instance in the Tokens page.
tower.enabled: Enable workflow monitoring with Seqera Platform (default: false).
tower.endpoint: The endpoint of your Seqera Platform instance (default: https://api.cloud.seqera.io).
tower.workspaceId: The workspace ID in Seqera Platform in which to save the run (default: the launching user’s personal workspace).; The workspace ID can also be specified using the environment variable TOWER_WORKSPACE_ID (config file has priority over the environment variable).

`trace`

The trace scope controls the layout of the execution trace file generated by Nextflow.

The following settings are available:

trace.enabled: Create the execution trace file on workflow completion (default: false).
trace.fields: Comma-separated list of trace fields to include in the report.
trace.file: Trace file name (default: 'trace-<timestamp>.txt').
trace.overwrite: Overwrite any existing trace file with the same name (default: false).
trace.raw: Report trace metrics as raw numbers where applicable, i.e. report duration values in milliseconds and memory values in bytes (default: false).
trace.sep: Character used to separate values in each row (default: \t).

`wave`

The wave scope provides advanced configuration for the use of Wave containers.

The following settings are available:

wave.enabled

Enable the use of Wave containers (default: false).

wave.endpoint

The Wave service endpoint (default: https://wave.seqera.io).

wave.freeze

New in version 23.07.0-edge.

Enable Wave container freezing (default: false). Wave will provision a non-ephemeral container image that will be pushed to a container repository of your choice.

The target registry must be specified using the wave.build.repository setting. It is also recommended to specify a custom cache repository using wave.build.cacheRepository.

Note

The container registry authentication must be managed by the underlying infrastructure.

wave.mirror

New in version 24.09.1-edge.

Enable Wave container mirroring (default: false). Wave will mirror (i.e. copy) the containers in your pipeline to a container registry of your choice, so that pipeline tasks can pull the containers from this registry instead of the original one.

The mirrored containers will have the same name, digest, and metadata.

The target registry must be specified using the wave.build.repository setting.

This option is only compatible with wave.strategy = 'container'. It cannot be used with wave.freeze.

Note

The container registry authentication must be managed by the underlying infrastructure.

wave.strategy

The strategy to be used when resolving multiple Wave container requirements (default: 'container,dockerfile,conda').

wave.build.cacheRepository

The container repository used to cache image layers built by the Wave service.

The corresponding credentials must be provided in your Seqera Platform account.

wave.build.compression.mode

New in version 25.05.0-edge.

The compression algorithm that should be used when building the container. Allowed values are: gzip, estargz and zstd (default: gzip).

wave.build.compression.level

New in version 25.05.0-edge.

Level of compression used when building a container depending the chosen algorithm: gzip, estargz (0-9) and zstd (0-22).

wave.build.compression.force

New in version 25.05.0-edge.

Forcefully apply compression option to all layers, including already existing layers (default: false).

wave.build.conda.basePackages

One or more Conda packages to be always added in the resulting container (default: conda-forge::procps-ng).

wave.build.conda.commands

One or more commands to be added to the Dockerfile used to build a Conda based image.

wave.build.conda.mambaImage

The Mamba container image is used to build Conda based container. This is expected to be micromamba-docker image.

wave.build.repository

The container repository where images built by Wave are uploaded.

The corresponding credentials must be provided in your Seqera Platform account.

wave.httpClient.connectTimeout

New in version 22.06.0-edge.

The connection timeout for the Wave HTTP client (default: 30s).

wave.httpClient.maxRate

New in version 25.01.0-edge.

The maximum request rate for the Wave HTTP client (default: 1/sec).

wave.retryPolicy.delay

New in version 22.06.0-edge.

The initial delay when a failing HTTP request is retried (default: 450ms).

wave.retryPolicy.jitter

New in version 22.06.0-edge.

The jitter factor used to randomly vary retry delays (default: 0.25).

wave.retryPolicy.maxAttempts

New in version 22.06.0-edge.

The max number of attempts a failing HTTP request is retried (default: 5).

wave.retryPolicy.maxDelay

New in version 22.06.0-edge.

The max delay when a failing HTTP request is retried (default: 90s).

wave.scan.allowedLevels

New in version 24.09.1-edge.

Comma-separated list of allowed vulnerability levels when scanning containers for security vulnerabilities in required mode.

Allowed values are: low, medium, high, critical.

This option requires wave.scan.mode = 'required'.

wave.scan.mode

New in version 24.09.1-edge.

Enable Wave container security scanning. Wave will scan the containers in your pipeline for security vulnerabilities.

The following options can be specified:

'none': No security scanning is performed.
'async': The containers used by your pipeline are scanned for security vulnerabilities. The task execution is carried out regardless of the security scan result.
'required': The containers used by your pipeline are scanned for security vulnerabilities. The task is only executed if the corresponding container is free of vulnerabilities.

`workflow`

New in version 24.10.0.

The workflow scope provides workflow execution options.

The following settings are available:

workflow.failOnIgnore

New in version 24.05.0-edge.

When true, the pipeline will exit with a non-zero exit code if any failed tasks are ignored using the ignore error strategy (default: false).

workflow.onComplete

Specify a closure that will be invoked at the end of a workflow run (including failed runs). See Workflow handlers for more information.

workflow.onError

Specify a closure that will be invoked if a workflow run is terminated. See Workflow handlers for more information.

workflow.output.contentType

Currently only supported for S3.

Specify the media type, also known as MIME type, of published files (default: false). Can be a string (e.g. 'text/html'), or true to infer the content type from the file extension.

workflow.output.copyAttributes

New in version 25.01.0-edge.

Currently only supported for local and shared filesystems.

Copy file attributes (such as the last modified timestamp) to the published file (default: false).

workflow.output.enabled

Enable or disable publishing (default: true).

workflow.output.ignoreErrors

When true, the workflow will not fail if a file can’t be published for some reason (default: false).

workflow.output.mode

The file publishing method (default: 'symlink').

The following options are available:

'copy': Copy each file into the output directory.
'copyNoFollow': Copy each file into the output directory without following symlinks, i.e. only the link is copied.
'link': Create a hard link in the output directory for each file.
'move': Move each file into the output directory.; Should only be used for files which are not used by downstream processes in the workflow.
'rellink': Create a relative symbolic link in the output directory for each file.
'symlink': Create an absolute symbolic link in the output directory for each output file.

workflow.output.overwrite

When true any existing file in the specified folder will be overwritten (default: 'standard').

The following options are available:

false: Never overwrite existing files.
true: Always overwrite existing files.
'deep': Overwrite existing files when the file content is different.
'lenient': Overwrite existing files when the file size is different.
'standard': Overwrite existing files when the file size or last modified timestamp is different.

workflow.output.storageClass

Currently only supported for S3.

Specify the storage class for published files.

workflow.output.tags

Currently only supported for S3.

Specify arbitrary tags for published files.

For example:

workflow.output.tags = [FOO: 'hello', BAR: 'world']

Configuration options

Unscoped options

apptainer

aws

azure

charliecloud

conda

dag

docker

env

executor

Executor-specific defaults

Executor-specific configuration

fusion

google

k8s

lineage

mail

manifest

nextflow

notification

podman

report

sarus

shifter

singularity

spack

timeline

tower

trace

wave

workflow

`apptainer`

`aws`

`azure`

`charliecloud`

`conda`

`dag`

`docker`

`env`

`executor`

`fusion`

`google`

`k8s`

`lineage`

`mail`

`manifest`

`nextflow`

`notification`

`podman`

`report`

`sarus`

`shifter`

`singularity`

`spack`

`timeline`

`tower`

`trace`

`wave`

`workflow`