Hi Nextflow people, just a small shameless promo from our side. We ran into a pretty annoying issue with deeptools

bamCoverage

on larger BAMs — jobs running for days and sometimes not even finishing with a usable bigWig. That got frustrating enough that we ended up writing our own thing in Rust: https://github.com/stela2502/bam_tide It basically does BAM → bigWig, nothing fancy, just… actually finishes. On the same data where deeptools struggled for days, this one took a few hours. Not saying it replaces everything, but if coverage is a bottleneck in your pipelines it might be worth a try. Would be interesting to hear if others have hit similar issues.

Go ahead and make a bioconda-recipe for it, and then we'll also create an nf-core module, for easier adaptation ;)

I can also recommend https://nf-co.re/modules/perbase/ for that kind of job.