Closed
Description
At the moment, if used with --singularity then nf-core download expects there to only be a single container and pulls that. There are however some pipelines that need more than one (sarek, neutronstar and more) and there will be many more (all) in the future.
Need to instead parse all instances of process.container if possible and automatically pull all required singularity images.
Would be good to combine with #464 to also automatically configure the pipeline with paths so that it knows where these containers are out of the box.