Unify iGenomes index usage

It appears that we are staging the index files from the standard igenomes.config in different ways in different pipelines. It would be nice to unify this and to use the same logic in the pipeline code. It can often be a source of confusion and I think its about time we come up with a robust solution.

One possible solution is to add the index prefix in igenomes.config for all types of indices (this is only done for BWA at the moment):
https://github.com/nf-core/tools/blob/d4354064bd5c237df9a8d98d09a3c87064f7be79/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/conf/igenomes.config#L15

and then to split the path into a directory and prefix in the pipeline code so the directory can be staged. This is flexible to custom user-provided paths, instances where the index may be named differently to the genome fasta and works on AWS where globs may not resolve all of the other files in the index (e.g. genome.fa*; @MaxUlysse ?).
https://github.com/nf-core/chipseq/blob/21be3149542cdc84431e12d1e092359058aed32a/main.nf#L168-L183

It would be nice if we can update and use a single igenomes.config across all pipelines if possible i.e. updating the template version and having this rolled out to pipelines via the automated sync. May be worth adding in Bowtie 1 index paths used in smrnaseq (Ping @lpantano). Also, ping @maxibor who is using Bowtie2 in coproid.

Start with the template igenomes.config and the referenced nf-core/chipseq main.nf sections to compare how index paths are configured and staged. Review how template updates are synchronized to pipelines, including the Bowtie 1 and Bowtie2 cases mentioned, and consider the work complete when pipelines use one consistent approach for standard and custom index paths.