Compatibility issue when using Micromamba instead of Conda for running kgwasflow on HPC cluster #44
Description
Hi,
I'm currently using kGWASflow on an HPC environnement (Nautilus cluster) where we use Micromamba as our conda-like environnement manager instead of Conda or Miniconda.
When i run the following command:
kgwasflow run -t 6 -d /scratch/nautilus/users/noraa/tmp_kgwasflow --configfile /LAB-DATA/GLiCID/users/noraa/kgwasflow_run/config/config.yaml --cores 10
The pipeline fails to execute correctly and the issue appears related to the way environnements are handled in the Snakefile--possibly due to compatibility assumptions about Conda/Miniconda that don't hold with Micromamba.
Have you tested kGWASflow with Micromamba ? Do you have any recommendations or worarounds for using Microamamba with Snakemake-based workflows in this context ?
Thanks in advance for your help!
Nouara,