Using --unsquash with singularity

[kenneditodd]

Hello,

I am trying to run the MOP2 Nextflow pipeline. I am new to using nextflow but am learning a lot as I go. I am submitting jobs to a cluster using slurm. The admins intentionally left squashfuse off the node. I keep getting the error message below.

FATAL:   container creation failed: mount hook function failure: mount /proc/self/fd/3->/usr/local/biotools/apptainer/apptainer-1.1.4/var/apptainer/mnt/session/rootfs error: while mounting image /proc/self/fd/3: squashfuse not found

I see that there is a --unsquash option with singularity exec. I am trying to add the unsquash argument to the apptainer scope with runOptions. However, I'm not sure the best place to put this. There are two potential config files to add this to - I have a nextflow.global.config and a slurm.config.

Where would I add the following code so I can submit to SLURM? I think it may look like one of the two ideas shown below but have had no success. Could be an issue with my syntax or placement.

containerOptions =  'unsquash'

or

apptainer {
     runOptions = '--unsquash'
}

[bentsherman]

You probably need to use apptainer.engineOptions. Either config file is fine, just depends on whether you want it to apply to all runs with apptainer or only with your SLURM system.