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

nf-core

Hi!
I have a question about *bwa-mem2+samtools* usage
I’m wondering are there any good solutions from nf-core not just install each module separately
```bwa index, bwa mem, samtools view, samtools sort, samtools index```
but use pipes in one module like
```bwa index | bwa mem | samtools view | samtools sort | samtools index```
because it saves space and basically works very good and quick with piping outputs between those tools?

maybe not the best place to ask but I feel people here should have enough knowledge using bwa + samtools…

I do think index and mem should be separate

<https://github.com/nf-core/modules/blob/master/modules/nf-core/bwamem2/mem/main.nf>

It does bwamem2 + samtools view or sort and can produce bam/cram and indexes

I do recognize that piping these modules would be sub-efficient, which is why we grouped some basic logic