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

nf-core

Hey Y'all

When running fq2bam manually (on a dedicated RTX 6000 Ada), via the docker run command, I can successfully process a one of the paired pod5 files. This uses 39GB of my 48GB graphics RAM.
 The sample was sequenced across 4 lanes. When I try to use Sarek to run fq2bam, I apparently run out of memory. I reduced the number of bwa streams to 2 from 4, using the custom config script <https://nf-co.re/sarek/3.8.1/docs/usage/#using-gpu-accelerated-alignment---aligner-parabricks|here>.

Is there anything else I can do to make it run?

I changed bwa streams to 1, and now it runs successfully.

You could also try setting the memory limit via the ext.args

```--memory-limit ```

Ah yes, thanks. Perhaps it will run faster with more streams then?