charliecloud

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

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.