Singularity
Singularity is the most widely used container system for HPC. The configuration file of the pipeline allows the automatic download of the image from Docker hub.
Offline use
Several HPC are kept off-line, so it's convenient to pre-download the Singularity image.
wget "https://warwick.s3.climb.ac.uk/ifrqmra-metaphage/v1.0/metaphage.simg"
Running with Singularity (manually)
Nextflow can be run using a Singularity image adding -with-singularity $PATH_TO_IMG to the command, for example:
nextflow run MetaPhage/main.nf -c project.config -with-singularity $PATH_TO_SIMG
Running with Singularity (configuration)
A simpler way to specify the container is with a configuration file, for example:
singularity.enabled = true
process.container = 'metaphage.simg'
singularity.autoMounts = true
If the image is saved in the directory specified in $NXF_SINGULARITY_CACHEDIR it's not necessary to add the path to the container, but just the container filename.