I also use a subworkflow in this workflow, but for a different purpose (the subworkflow is also on Github: https://github.com/DarwinAwardWinner/hg38-ref). But subworkflow rules are still resolved as part of the same DAG, so they have the same issue. Hence the need for a separate pre-workflow outside the normal framework of Snakemake.
By the way, I guess I didn't add a comment explaining this, but the reason for using the processify decorator is that the snakemake API is not re-entrant, so calling `snakemake` from within a Snakefile normally breaks things. The solution is to call it in a separate process.
By the way, I guess I didn't add a comment explaining this, but the reason for using the processify decorator is that the snakemake API is not re-entrant, so calling `snakemake` from within a Snakefile normally breaks things. The solution is to call it in a separate process.