Container usage

PARANOiD offers the usage of docker containers via several different executors.
Currently supported executors are Docker, Podman, and Singularity.
Since containers are handled via Nextflow, the download should start automatically when running the pipeline.
The default directory for images is inside the work directory created 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 comma (e.g. -profile apptainer,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

Apptainer

Uses Apptainer to run processes within containers

-profile apptainer