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

nf-core

Screenshot 2026-06-24 at 11.28.27.png

Another question: It fails towards the end where I get an error that the disk quota is exceeded and I think it's about the singularity cache

Should I specify the cachedir in some way so it's not using from my user quota (it looks like it's by default put there) but from the storage project quota

+ should I then both set the NXF_SINGULARITY_CACHEDIR and the NXF_APPTAINER_CACHEDIR or only the former?

It doesn't hurt to set both, but `NXF_SINGULARITY_CACHEDIR` should be the important one (or having a `nextflow.config` that does the corresponding thing).

Something like this:
`export NXF_APPTAINER_CACHEDIR=/cfs/klemming/projects/snic/uppstore2017270/common_tools/NF-CORE_PANGENOME_APPTAINER_CACHEDIR`
`mkdir -p $NXF_APPTAINER_CACHEDIR`

`export NXF_SINGULARITY_CACHEDIR=/cfs/klemming/projects/snic/uppstore2017270/common_tools/NF-CORE_PANGENOME_SINGULARITY_CACHEDIR`
`mkdir -p $NXF_SINGULARITY_CACHEDIR`

Looks good.

(The profile is currently set to use the `singularity` container engine and thus should pick up that option, but for the jobs, we're loading the `apptainer` module and relying on that to provide the `singularity` binary :slightly_smiling_face:

Any reason it's the apptainer module and not the singularity one?

Yes, it's due to how PDC had built the tooling (at least at some earlier point in time).

Can I safely remove the `.singularity` and `.apptainer` directories in my home directory that currently takes up quite some space?

The singularity provided would unpack the container images whereas the apptainer setup would mount them  (only using what's needed).

Yes, they're fine to remove. They will be recreated though.

Yeah, but with less things in them if I remember to set the cache dirs elsewhere from now, right

Ok, testing again. It almost reached the end yesterday, it failed on the last multiqc step where it's collecting all stats :face_palm: