NextFlow and Apptainer

[Elisabeth Ortega]

Hi all,

I'm trying to run a simple pipeline using an apptainer in a local environment. To do so, I used two different approaches:

- Approach A: running "apptainer exec blablabla" in the pipeline (nf file).

- Approach B: writing the command to execute in the nf file and the needed environment vars,  and using -with-singularity option.

The Approach A works as expected (getting the same result executing it in nextflow and in the local machine direclty) but the approach B fails in a non-sense step (is asking for a file that is not generated in this run and in the "working" approach).

More extra information that may help or not: I'm trying to execute an OpenFoam workflow in two steps (long story...). 

My question here is if I'm missing something in the usage of singularity in nextflow. I thought that the option -with-singularity is just adding "apptainer/singuilarity exec blabla.sif" at the beggining of the .command.sh script.

Thanks in advance for your help here!

Elisabeth

[Paolo Di Tommaso]

Nextflow does not have a built-in support for Apptainer.  

I'm wondering if Apptainer command line is compatible with Singularity. If that's the case you can just create a simlink "singulairty" -> "apptainer" and it should work 

p

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