Is there a way to get the rules submitted to the cluster to inherit the parent command singularity container?
I’m running the base snakemake within a container for portability with most rules using other conda envs. So I can create the base conda env with snakemake and all the rule conda envs within the container. This works fine for running everything locally, all the rule conda envs were created within the container, so can be found. But when using cluster submission, the shell script is executed independent from the parent container, so fails. Is there a way to pass the parent singularity container to the submitted jobs?

Do I need a custom cluster submission script?

The alternatives are using individual singularity containers for each rule or containerize for the whole workflow, but this doesn’t include the parent snakemake env itself.