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:

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

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).

Edited by Alex Kanitz
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