Input naming conventions

[edmundmiller]

Follow up to https://github.com/nf-core/modules/pull/1437#discussion_r834774713

We currently use reads for unaligned reads(fastq), and then bam for the aligned reads, but this doesn't cover cram, and sam.

It also doesn't cover things like when a bam or a bed file are possible.

I personally think input is a little too vague to name the variable as well.

[FriederikeHanssen]

as mentioned in the other PR I like

aligned_input or input_aligned for bam/cram/sam and then aligned_index for bai/crai/sai

[maxulysse]

as usual @FriederikeHanssen is right on point

[rpetit3]

For modules that download a database, a naming convention would be great.

I've seen download, update, and setupdb. But I also understand some of these might actually be the names of the subcommand to download the database (e.g. amrfinder_update)

[edmundmiller]

I don't know what effect #1338 might have on this, but it might solve some of it.