Hi ! Can I have a review for bcftools/mpileup ? https://github.com/nf-core/modules/pull/10951

For me conceptually, if we want: fasta, fai, gzi then we actually should have fasta, fasta_gz, fai, gzi. And actually this is much simpler: fasta, index So I would just tidy up the names and not change much of the current structure

Ah, I didn't knew the

.gzi

, replaced the

.fai

for compressed fasta. I thought this was an additional necessary file. If it's the case it is indeed easier to use fasta, index format !

@Matthias De Smet correct me if I'm wrong here please 🙏

faidx

manual states

--gzi-idx FILE
Read/Write to specified compressed file index (used with .gz files).

Thanks this will be easier for me !

I would also approve if this we’re a bulk PR that fixes this for all the

bcftools

modules 😉

I think we should actually check what we have done in the modules repo and maybe fix the other modules that have multiple indexes

Seems like a hackathon project in itself 😅