Oxli prototype using fastq-to-fasta

- [ ] Is it mergable?
- [x] Did it pass the tests?
- [x] If it introduces new functionality in scripts/ is it tested?
  Check for code coverage.
- [x] Is it well formatted? Look at `make pep8`, `make diff_pylint_report`,
  `make cppcheck`, and `make doc` output. Use `make format` and manual
  fixing as needed.
- [x] Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment. 
- [x] Is it documented in the ChangeLog?
- [x] Was a spellchecker run on the source code and documentation after
  changes were made?
Fwoa, what a mess! What ideas do you have to refactor this?