Discussion: add random seeds to scripts

[jashapiro]

I realized that some of the filtering we are doing (emptyDrops and miQC, notably) do/may have statistical models that are fit with some random components. Should we alleviate any variation from this by adding fixed random seeds to the relevant scripts?

[jaclyn-taroni]

If this was outside of the context of a project like this (e.g., I was working with a single dataset), I might run things multiple times with different seeds to make sure there was some semblance of stability in my results and then set a seed for reproducibility. Taking that approach doesn't really make sense here. I don't have an answer so much as a series of questions/prompts:

• Does setting a seed improve our ability to debug things? Which I will extend to include update versions of software without going, "Hm, maybe it was just the seed?"
• If we set a seed, do we need to communicate to our users that we haven't done what I describe above (i.e., what we give to them may not be representative of multiple runs)?
• And perhaps most importantly: what degree of variability are we expecting? Depending on the answer, is it better to write tests instead?

[jashapiro]

closed by #50