We should include a CITATION file in the main repository to indicate how to cite the pipeline.
To have a proper scientific publication, we could write a publication in the "Journal of Open Source Software".
That way, the pipeline could be properly cited. Publications are short ~3 pages and easy to write.
See an example:
http://joss.theoj.org/papers/6eb3ba7dddbdab8788a430eb62fc3841
Citation would look like:
Bennett et al., (2018). restez: Create and Query a Local Copy of GenBank in R. Journal of Open Source Software, 3(31), 1102, https://doi.org/10.21105/joss.01102