feat(Execution workflows / Utils): making RefSeq annotations work for QAPA and PAQR.

In trying to run the more conservative RefSeq annotation on certain tools, I've run in to an issue where the tools assume specific attributes (e.g. Ensembl type attributes for [QAPA](https://github.com/morrislab/qapa#prepare-annotation-files) or Ensembl/Gencode for [PAQR](https://github.com/iRNA-COSI/APAeval/tree/main/execution_workflows/PAQR#annotation-dependent)) to be present in order to build their annotation.

I need to check a bit deeper to make sure I gather all the requirements. Not sure if it is best to make a Util script to transform a RefSeq gtf so it contains theses required Ensembl/Gencode attributes or if we should add an option within each EWF to handle this.