Tim Booth

> The conda_env.yaml file contains a whole lot of specific packages. > Consider filtering this to specify just those packages you would install > manually: snakemake, fastqc, kallisto, etc. Let...

From @cmeesters: the environment file is frighteningly complex: too many dependencies are defined explicitly - conda (and its implementations) are defined to resolve dependencies automatically. Please restrict yourself to the...

> the environment file is frighteningly complex: too many dependencies are defined explicitly - conda > (and its implementations) are defined to resolve dependencies automatically. > Please restrict yourself to...

> versions are pinned for Snakemake and other dependencies, rather than defining minimum versions >=. > The way it is, becoming outdated is only a question of time. Pinning the...

> As Snakemake recommends mamba, mamba should be mentioned, too. My understanding is that the explicit `mamba` command is obsolete, so if the Snakemake documentation is still recommending running `mamba`...

> new users should be introduced into creating separate environments, a conda environment > can be created with the required files in one command This option is addressed in episode...

Additionally from @cmeesters > the directory for conda/mamba/micromamba does not need to be created, deviating from the > standard setup is not necessary. I've removed the `mkdir` command. I guess...

As far as the minimal environment specs are concerned, they are here: https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/files/conda_env_min.yaml This file isn't new, but its not currently linked in the setup page because what I did...

I have fixed the frozen Conda environment to use a more compatible version of Kallisto. Fortunately I was able to do this without changing any of the other software versions,...

I had a look at the standard for docstrings, which are a common Python example of multi-line strings (https://peps.python.org/pep-0257/) but that simply says putting a newline right after the opening...