I'm having trouble that after the workflow has run, it keeps trying to regenerate files that are already present. I think this wasn't an issue before because this is a change that happened in snakemake at the end of May 2022 (https://github.com/snakemake/snakemake/issues/1694).
It didn't affect our code until I merged my fork of snakemake with the main branch a few weeks ago.
I can get the code to work by adding --rerun-triggers mtime at the command line. We need to work out what is triggering snakemake to want to rerun these rules.
I'm having trouble that after the workflow has run, it keeps trying to regenerate files that are already present. I think this wasn't an issue before because this is a change that happened in snakemake at the end of May 2022 (https://github.com/snakemake/snakemake/issues/1694).
It didn't affect our code until I merged my fork of snakemake with the main branch a few weeks ago.
I can get the code to work by adding
--rerun-triggers mtimeat the command line. We need to work out what is triggering snakemake to want to rerun these rules.