snakemake-software-deployment-plugin-container 0.2.0

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snakemake-software-deployment-plugin-container

A generic container plugin implementing snakemake's software-deployment interface.

• It executes the given commands within a rootless container.
• It currently supports both udocker and podman.

Usage

The kind parameter specifies valid values for the container runtime to use.

The container directive (should be) used to specify the container image to use for the software deployment. This string should be a valid container image name, including the tag; e.g., biocontainers/example:1.0.

By default, the plugin will attemtp to use 'latest' tag if no tag is provided. However, be aware that some registries may not support this, for good reasons having to do with reproducibility. So, it's a good idea to specify a tag.

Status

• Work in progress. The plugin conforms to the current software-deployment interface specification, and it has passing tests.
• Will revisit when further work is done in snakemake core to allow a more reusable integration of deployment plugins.

TODO

• Add support for apptainer
• Implement repot_sofware method with container URI and the resolved hash of the image.