It is important that computational biology work is made with documentation and replicability in mind. This helps not only colleagues who need to replicate your work, but it also helps you when it comes time to write up the work for a paper.
These are versioned, shareable and replicable proteogenomics workflows that I have used during my PhD. This repository forms half of my proteogenomics lab notebook. The other (private) half records exactly what was run and which datasets were used. I'm not in a position to share the details of the analysis at the moment, but I think that the nextflow workflows and Docke images might be of use to other people.