amend

profiles/apptainer/local/config.yaml

@@ -13,7 +13,7 @@ keep-incomplete: true # true only for debugging
 use-conda: true # Omitting this line was the culprit, now the 'snakemake --containerize' auto stuff works!
 use-singularity: true
 # What happens if I don't define the singularity-prefix? Does it download the image to the running directory of the alias?
-singularity-prefix: '~/.asscom2/apptainer-prefix' # Directory in which singularity images will be stored. Couldn't find a way of using the $ASSCOM_BASE system variable.
+#singularity-prefix: '~/.asscom2/apptainer-prefix' # Directory in which singularity images will be stored. Couldn't find a way of using the $ASSCOM_BASE system variable.
 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