singularity
The singularity scope controls how Singularity containers are executed by Nextflow.
singularity.autoMounts
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
Requires Singularity 3.11 or later
When enabled, OCI (and Docker) container images are pulled and converted to the SIF format by the Singularity run command, instead of Nextflow (default: false).
Leave ociAutoPull disabled if willing to build a Singularity native image with Wave (see Build Singularity native images).
singularity.ociMode
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).
Leave ociMode disabled if you are willing to build a Singularity native image with Wave (see Build Singularity native images).
singularity.pullTimeout
The amount of time the Singularity pull can last, after which the process is terminated (default: 20 min).
singularity.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://.
singularity.resourceLimits
Apply the task cpus and memory directives as container resource limits using the --cpus and --memory flags (default: false).
singularity.runOptions
Specify extra command line options supported by singularity exec.