Singularity container execution of pangolin crashes with recent nextflow versions about porecov

[replikation]

ah "OSError: [Errno 30] Read-only file system: '/home/'"

is a singularity error @hoelzer can you tune in you had this OS errors before

[replikation]

maybe the answer with the --writable helps for singularity:

https://stackoverflow.com/questions/65599721/unable-to-build-writable-singularity-container

[MarieLataretu]

I'm wondering why this error occurs (only?) with the pangolin container. Apparently, it needs to have access to home?

@Krannich479, did you also try setting NXF_SINGULARITY_HOME_MOUNT to true with a recent Nexflow version?

[replikation]

based on the error pangolin wants to write something in its own container home directory. and singularitys home is not writable. as far as i understand (?) but this is something that the user controls with its own singularity system. it could be that however, we need to add as a flag to the config or so

[hoelzer]

Uff... yes that is annoying and someone else here had this problem recently - for me it still worked bc my nf version is 22.x.x or so.

I am not sure what is happening inside the pangolin container but yeah, the problem is that pangolin wants to write something in /home which is fine with a encapsulated Docker container but fails with Singularity. Because here the process actually tries to write in the HPC system path.

[Krannich479]

@Krannich479, did you also try setting NXF_SINGULARITY_HOME_MOUNT to true with a recent Nexflow version?

Tried this, didn't work for me :/