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7 changes: 7 additions & 0 deletions docs/lrz_cm4.md
Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,13 @@ micromamba create \
micromamba activate nf-env
```

Depending on the pipeline, it may additionally be necessary to load the `squashfs` module.
This is required when Apptainer needs to build or convert container images locally at runtime (e.g. when pulling from Docker Hub), as it relies on the `squashfs-tools` userspace utilities (`mksquashfs`/`unsquashfs`). Pipelines that use pre-built `.sif` images directly do not require this.

```bash
module load squashfs
```

## Considerations

While testing can be done with partial nodes, or interactive jobs, we recommend requesting at least one full node for production runs. Both `local` and `flux` executor can be used for single-node runs, multi-node runs **must** use `flux` to make use of the additional resources. Please note that during testing, we observed that the same test-run of `nf-core/rnaseq` took around 11h with the `local` executor, and 8h with the `flux` executor, which we largely attribute to more efficient scheduling.
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