Nicolas Vannieuwkerke

The option has been added!

Thank you for the thorough answer, I'll try to find a workaround in the meantime

Hi can you try binding the directory with your input files and annotations directory to the container? This can be done with `--bind` (see [here](https://docs.sylabs.io/guides/3.0/user-guide/bind_paths_and_mounts.html#user-defined-bind-paths) for more information about this).

I'm using it in a nextflow pipeline on an HPC cluster and it works perfectly for me...

Nextflow arranges the execution of singularity containers internally, so I'm not sure it'll help you, but here is the code that does the execution of AnnotSV: https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-structural/blob/add-expansionhunter/modules/nf-core/annotsv/annotsv/main.nf

I'm not sure either why it's not working for everyone else. I didn't create the container myself (it's automatically generated via bioconda). Maybe you could ask more info on the...

Have you tried converting the docker container to a singularity image? maybe this could work?

Hi @ManavalanG and @lgmgeo, the reason `make install-human-annotation` couldn't be run in the recipe is that it would make the recipe very large (which is a bad practice in bioconda)....

Looks good to me! I'm all for it as long as this will still work to create a separate folder of the annotations

It's weird that this file isn't in the recipe because it uses an exact copy of the repository. I can have a look when you release the new version :)