Container usage

PARANOiD offers the usage of docker containers via several different executors.

Currently supported are Docker, Podman and Singularity.

As containers are handled via Nextflow the download should start automatically when running the pipeline.

The default directory for images is within the work directory generated by Nextflow.

If problems occur while downloading images via Nextflow the script pull_images.sh can be used to preload them.

It is recommended to run PARANOiD with containers to ensure correct versioning of tools.

If several profiles are used (e.g. using singularity together with SLURM) they are separated by a single , (-profile singularity,slurm)

Docker

Uses Docker to run processes within containers

-profile docker

Podman

Uses Podman to run processes within containers

-profile podman

Singularity

Uses Singularity to run processes within containers

-profile singularity