apptainer
The apptainer scope controls how Apptainer containers are executed by Nextflow.
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
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).
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.resourceLimits
Apply the task cpus and memory directives as container resource limits using the --cpus and --memory flags (default: false).
apptainer.runOptions
Specify extra command line options supported by apptainer exec.