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Files cached with workflow.source_path are not available in apptainer #3361

@johausmann

Description

@johausmann

Is your feature request related to a problem? Please describe.

When a rule uses an auxiliary source file provided with the workflow and references it with workflow.source_path(), the file is not accessible in the apptainer/singularity container

Describe the solution you'd like

The referenced files are cached by snakemake. The paths to the snakemake cache folder (probably defined by $XDG_CACHE_HOME) should be mounted when running the command.

Describe alternatives you've considered

Currently, the user has to bind e.g. /home/$USER/.cache/snakemake/ to the container via the --apptainer-args command line option.

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