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?
Not sure. We could create classes for these scripts and use them as objects and assign values to their attributes upon creation; we could change it so instead of passing loads of individual arguments we could pass in a single collection of args but that's rather close to the previous iteration of the prototype worked and we nixxed that. 

Personally I'd prefer to do something object-y. Seems.. Intuitive, almost.