# Resources

cores: all


# Policies
keep-going: true 


keep-incomplete: true # true for debugging
rerun-triggers: "mtime" # Only rerun on changes in modification time. Not on code hash changes.





# Apptainer
use-conda: true # Omitting this line was the culprit, now the 'snakemake --containerize' auto stuff works!
use-singularity: true
# If you don't define a common singularity-prefix, the image will be pulled every single time
singularity-prefix: "~/.asscom2/singularity-prefix" # Directory in which singularity images will be stored. Couldn't find a way of using the $ASSCOM_BASE system variable, so users should manually change this here if they want to use something else.
singularity-args: "--bind $ASSCOM2_BASE,$ASSCOM2_DATABASES" # Must also bind ASSCOM2_BASE so we can access databases and report scripts etc. When this issue is solved I'll add individual arguments to rules and make it more flexible https://github.com/snakemake/snakemake/issues/262

# Comments for the singularity-args parameter. I don't know why the necessary /opt/conda/bin path, which is present when I run the image, is gone when snakemake runs. Also, since the databases are likely in a soft linked directory, you must bind it if you want access

# Local setup for a typical workstation
# resources:
#   - mem_mb=122000
