DSL2 pipeline

We need to deploy the new version of the pipeline DSL2. The current DSL1 is not compatible with the new versions of nf-core. Tasks: 

- [ ] Create a branch called `pgdb-dsl2` in  https://github.com/bigbio/pgdb 
- [ ] Merge the DSL2 version into DEV in bigbio 
- [ ] Include the new versions of pypgatk 
- [ ] Test with new datasets. 
- [ ] Merge the final version into nf-core. 


