Fill in a workflow

We have a workflow with missing information in some rules, marked as ???. The goal is to fill them in.

There are two flavours of the workflow. Start with the fixme file in the easier folder; the one in the harder folder is more involved.

Test what you filled in works by using the -n flag.

Actually run using

snakemake --use-conda -j 4

The --use-conda directive is not actually needed here, but can be used to build custom conda environments for specific rules. In this case the environment we created contains everything needed for all rules already.