Wire all rules with Snakefile

Problem

Currently, there are almost a dozen closed issues for rules to be added to the workflow, suggesting that these rules are in principle in a state that should allow them to be included in the workflow:

• #7 (closed)
• #8 (closed)
• #9 (closed)
• #10 (closed)
• #11 (closed)
• #12 (closed)
• #13 (closed)
• #14 (closed)
• #15 (closed)
• #16 (closed)
• #17 (closed)

However, the latest DAG representation suggests that only a fraction of these rules are currently wired into the main Snakefile or a subworkflow thereof:

Possible solution

Go through the Snakefile and ensure that all available rules are called when starting a workflow run. Specifically, ire all rules of both paired end and single end pipelines with main Snakefile:

• paired end
• single end

Additional context

Close #6 (closed) once this issue is resolved, but make sure that specific issues exist for any unresolved points mentioned in that issue (see this comment).