search

snakemake / snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster
MIT License
18 stars 18 forks source link

--software-deployment-method argument has a different behaviour using CLI and profiles #151

Open ArthurDondi opened 1 month ago

ArthurDondi commented 1 month ago

Software Versions

snakemake 8.20.4 snakemake-executor-plugin-slurm 0.10.2 snakemake-executor-plugin-slurm-jobstep 0.2.1 slurm 23.02.7

Describe the bug Running snakemake with argument sdm: conda apptainer in profile/config.yml (I also tried with quotes, nested quotes, comma) in the config file leads to the following error: slurm_script: error: argument --software-deployment-method/--deployment-method/--deployment/--sdm: invalid choice: 'conda apptainer' (choose from 'apptainer', 'conda', 'env-modules

If I run it with --sdm conda apptainer as command line argument, it works. sdm: apptainer and sdm: conda also work in profile/config.yml, but not the combination.

cmeesters commented 1 month ago

Hm, definitively not related to the plugin code, as software deployment works in Snakemake's core. @johanneskoester a shortcoming whilst parsing, perhaps?