Configuration options

The Nextflow configuration is organized into config scopes. The following pages describe the available settings in each scope.

Each setting is listed by its fully qualified name, which includes the enclosing scopes. You can write a setting using either dot syntax or block syntax:

// dot syntax
docker.enabled = true
docker.runOptions = '-u $(id -u):$(id -g)'

// block syntax
docker {
    enabled = true
    runOptions = '-u $(id -u):$(id -g)'
}

See Blocks for more information about the two forms.

Config scopes

Page	Description
Unscoped options	Settings that are not part of a config scope.
appleContainer	Controls how Apple container is used by Nextflow.
apptainer	Controls how Apptainer containers are executed by Nextflow.
aws	Controls the interactions with AWS, including AWS Batch and S3.
azure	Controls the interactions with Azure, including Azure Batch and Azure Blob Storage.
charliecloud	Controls how Charliecloud containers are executed by Nextflow.
conda	Controls the creation of Conda environments by the Conda package manager.
dag	Controls the generation of the workflow diagram.
docker	Controls how Docker containers are executed by Nextflow.
env	Defines environment variables that are exported into the environment where tasks are executed.
executor	Controls various executor behaviors.
fusion	Provides advanced configuration for the use of the Fusion file system.
google	Controls the interactions with Google Cloud, including Google Cloud Batch and Google Cloud Storage.
k8s	Controls the deployment and execution of workflow applications in a Kubernetes cluster.
lineage	Controls the generation of lineage metadata.
mail	Controls the mail server used to send email notifications.
manifest	Defines pipeline metadata that is useful when publishing or running your pipeline.
nextflow	Controls the retry policy used for retryable operations.
notification	Controls the automatic sending of an email notification on workflow completion.
podman	Controls how Podman containers are executed by Nextflow.
registry	Configures the registries used to resolve modules and plugins.
report	Controls the generation of the execution report.
sarus	Controls how Sarus containers are executed by Nextflow.
seqera	Controls the interactions with Seqera services.
shifter	Controls how Shifter containers are executed by Nextflow.
singularity	Controls how Singularity containers are executed by Nextflow.
smolvm	Controls how smolvm microVMs are used by Nextflow.
spack	Controls the creation of Spack environments by the Spack package manager.
timeline	Controls the generation of the execution timeline.
tower	Controls the settings for Seqera Platform (formerly Tower Cloud).
trace	Controls the generation of the trace file.
wave	Provides advanced configuration for the use of Wave containers.
workflow	Provides workflow execution options.