Use RefGenie for pipeline template `genomes.conf` config

Split from #592 - specifically https://github.com/nf-core/tools/issues/592#issuecomment-804419834

I wanted to announce an update that would allow using refgenie for unarchived cloud assets directly. You first need a refgenie digest for the genome of interest, which you can get at an endpoint like this: http://rg.databio.org/genomes/genome_digest/hg38.

Then, you can use that with the assets/file_path endpoint to return either an http or s3 URL to the file of interest. For example:

• http://rg.databio.org/assets/file_path/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/fasta/fasta?remoteClass=s3
• http://rg.databio.org/assets/file_path/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/fasta/fasta?remoteClass=http

you can also use individual seek keys, just like the CLI, to get individual items within an asset:
http://rg.databio.org/assets/file_path/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/fasta/chrom_sizes?remoteClass=s3

One way to auto-generate a config file is to use the new refgenie populate function.

you would create a template like:

params {
  // illumina iGenomes reference file paths
  genomes {
    'GRCh37' {
      fasta       = "refgenie://hg38/fasta"
      bwa         = "refgenie://hg38/bwa_index"
      bowtie2     = "refgenie://hg38/bowtie2_index"
      }
    }
}

then you just run some flavor of refgenie populate file.tpl and you'd get the above, using the then-current URIs

So the idea would be to make a copy of the template conf/igenomes.conf file (need to rename to just genomes.conf) that is called conf/igenomes.conf.tpl. Then build that with the asset identifiers as described above.

Once that's done, we run refgenie populate on that file to create the conf/genomes.conf file with the absolute assets. This file should never be directly edited.

To ensure this, we should have a CI test that regenerates the file and checks that it matches what is committed to the repo (eg. git diff doesn't return anything).

Many / most of the reference genome assets that we currently have will be missing for now I guess, so this ties in with issue https://github.com/nf-core/tools/issues/1086 to create those. But we can leave them commented out and in a branch for now until they are ready.