A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I need to use `samtools view` with an index and a BED, but it appears to <https://github.com/nf-core/modules/blob/master/modules/nf-core/samtools/view/main.nf|not support both>? Am I missing something here?

e.g. `samtools view -o ${prefix}.bam -L ${bed} ${bam}`

AFAICT this has nothing to really do with taking an index? The module just isn’t set up to take a bed file of regions as input at all? Probably should be added as an optional input

Oops, yep I meant the other way around. 

_Sigh_ I really didn’t want to have to fix up another core module.