This PR contains three workflows:

lfq-clustering

Workflow performing clustering to improve spectral-counting data / infer additional identifications through clustering.

This workflow represents the one used in the paper (with some upgrades).

Once the new X!Tandem version is available on biocontainers the location of the container needs to be changed (currently points to my own container).

spectra-cluster-benchmark

This workflow is still work in progress and not yet complete. It's only included since I already committed the changes...

Reprocessing workflow. Uses X!Tandem + MSGF+ + PIA to process a set of MGF files

TODO:

The PIA configuration still needs work and should include the filters we discussed:
- remove differently identified spectra
- filter based on q = 0.01 for spectra identified by both engines
- filter based on q = 0.001 for spectra only identified by one engine)

Again, the X!Tandem container should finally point to the biocontainers container and not mine.