nf-core download interprets custom registry

[adamrtalbot]

Description of feature

Currently, nf-core download will not respect a custom registry which means it tries to pull from docker.io when a short container name is specified (e.g. org/tool:version). We should add the custom registry as a param. As an extension, it could interpret it from configuration files automatically.

[MatthiasZepper]

I think, the easiest solution would be to provide the registry right when the singularity command is being build:

tools/nf_core/download.py

Lines 1023 to 1029 in 711d074

	if shutil.which("singularity"):
	singularity_command = ["singularity", "pull", "--name", output_path, address]
	elif shutil.which("apptainer"):
	singularity_command = ["apptainer", "pull", "--name", output_path, address]
	else:
	raise OSError("Singularity/Apptainer is needed to pull images, but it is not installed or not in $PATH")
	log.debug(f"Building singularity image: {address}")

Since the old released pipelines do not adhere to the latest template, I think the nf-core download command could only check for a custom registry definition in $HOME/.nextflow/config or a $PWD/nextflow.config, but not consider pipeline specific configuration (although the pipeline repo is downloaded first, so it could be read from there as well)
Subsequently, that info could be used accordingly to modify the address to which the pull command is being directed.

Alternatively, we could also hardcode several standard registries with some sort of waterfall logic that the next registry is being tried if the previous one failed for whatever reason?

[mirpedrol]

Done with #2336 🎉