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

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ArthurDondi opened this issue Sep 20, 2024 · 1 comment

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

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