diff --git a/docs/lrz_cm4.md b/docs/lrz_cm4.md index 4e32ff965..3c188dace 100644 --- a/docs/lrz_cm4.md +++ b/docs/lrz_cm4.md @@ -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.