nf-core download: Handle multiple containers

[ewels]

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.

[maxulysse]

Could be an issue if the tag is specified by a parameter:
https://github.com/nf-core/sarek/blob/5c30fd821ab7cdf27fd4105464a1fba5eabdfcd5/conf/base.config#L67-L74
I could rewrite these lines to specify each containers for each genome, but then wouldn't nf-core download try to download all containers?
Then again, Sarek is a very specific case...

[apeltzer]

Yeah, I fear this is very special behaviour. Most people will (hopefully?) use biocontainers soon when DSLv2 is used more widely, then downloading directly from biocontainers instead...

[ewels]

Much of the download code was rewritten #832 - I think that having special cases like this is beyond the scope of nf-core download so I will close this issue now.