code comments

[yannickwurm]

• In the future, please use proper commit messages. Not "edited xxx.md" (that is a tautology! - but rather what change you made)

• 02-make_star_index.zsh has variables that I don't think would work. (e.g. <species>). or <max(ReadLength)-1>
• in 01-quality_control/ - things are exteremly fragmented. For example, runnign STAR is one concept and should thus be in one file, not split across multiple
• e.g., in 02-differential_expression_analysis/deseq2_bombus_harrison.Rmd do not tell the file to run elsewhere - this happens with setwd(dirname(rstudioapi::getActiveDocumentContext()$path)) and with renv::init(project = "~/projects/2020_bombus_nachrs". Instead, run the file (or an alias to the file) in the right place.
• you shouldn't be running renv::snapshot every time. You set things up once, then run snapshot. That snapshot file (renv.lock) should not change again within the project. Here instead, you are creating a new snapshot every time with the latest versions every time. Using renv also means that you don't need to have all the installation code, as it happens automagically with something along the lines of renv::restore(). You could move all that package installation stuff to a different file if you want to remember how you made the renv
• in something like glm_tpms_bombus_colgan.Rmd -indeed stick to a specific ensembl version.
• delete all commented lines