Pull Request Checklists

Important: When opening a pull request, keep only the applicable checklist and delete all other sections.

Checklist for New Module

[X] I used the cookiecutter template and updated the placeholder rules.
[X] The snakemake rules follow the design guidelines.
- [X] All references to the rules object (e.g. for input files) are wrapped with str().
[X] Every rule in the module is either listed under localrules or has the threads and resources directives.
[X] Input and output files are being symlinked into the CFG["inputs"] and CFG["outputs"] subdirectories, respectively.
[X] I grouped the input symlinking rule to the next job that uses the input files.
[X] I updated the final target rule (*_all) to include every output rule.
[X] I explained important module design decisions in CHANGELOG.md.
[X] I tested the module on real data for all supported seq_type values.
[X] I updated the default.yaml configuration file to provide default values for each rule in the module snakefile.
[X] I did not set any global wildcard constraints. Any/all wildcard constraints are set on a per-rule basis.
X ] I ensured that all symbolic links are relative and self-contained (i.e. do not point outside of the repository).
[X] I replaced every value that should (or might need to) be updated in the default configuration file with __UPDATE__.
[X] I recursively searched for all comments containing TODO to ensure none were left. For example:
```
grep -r TODO modules/<module_name>/1.0
```