Maxime U Garcia

You should be able to directly download the images hosted by galaxy, but I agree to get the singularity conversion of the dockerhub images you do need Singularity. Maybe it...

The way they do it in the GATK4 pipelines is to pass the reference.fasta file name as a string. We could pass the value as an additional entry, or have...

I'm sure we can hack the `find` line., but wouldn't it be easier and less hacky to have an extra value?

don't want to stage an extra fasta file, just the name

No, because I would only pass `BWAIndex/genome.fa`. To be honest I would only pass `genome.fa`, and use `{}` to cover all extension from the indices... but that's another debate...

I'm guessing the `UNTAR_STAR_INDEX` process (or any similar) could give out the indices, that we can collect to use as only one channel, and the value for the `genome.fa` or...

What do you think of something like that: https://github.com/MaxUlysse/nf-core_sarek/commit/35956ab3be9e09fea2142f7428a03ce8b4d30198

> I think that could work. > > To be honest though I don't know why the `INDEX` was introduced, so if someone could link that discussion I might be...

I think we can have a `bwaindex.first.basename()` or something like that to get the actual fasta name, and add that to the map in case of user specified indices

I'll look into it.