Tim Booth

The choice of *fastx* and *velvet* is deliberate. These tools are simple, stable, and serve the purpose of the tutorial which is to show how to orchestrate commands with Snakemake....

Also: > Kallisto performs (wording according to docs) a "pseuoalignment" - it is not a classical aligner and > should not be mentioned as such. Indeed - I'll correct this.

I have a fork of Snakemake 7 where I tried to eliminate as many `stat()` calls as possible: https://github.com/edinburghGenomics/snakemake It's not suitable for general consumption because it breaks some Snakemake...

I believe this is the same bug as per #2626 and #2011, and in brief summary: * The behaviour seen by @powelleric is correct/expected but not well documented (see for...

Yes it's annoying. Depending on your application you may find that always using `--drop-metadata` is a viable workaround. This does increase the risk of leaving partial output files if your...

Hi @Warggr I've been looking through this part of the code and I can see the problem. In fact, I can see a whole lot of problems. The code within...

Regarding the last three points, I completely agree that workflow re-use and maintainability is a vital topic and I'm currently in the process of preparing (and being funded to do...

> genome assembly is an intricate challenge, recommending a relatively outdated tool like velvet is > dangerous, as there are numerous follow-up implementation tailored for various genome types. I totally...

I have added clarification to the text regarding what the workflow is doing and the choice of tools. I have also added a section "Biology and bioinformatics" to `instructor/prereqs.html`. The...

I'm not convinced this topic fits into Episode 9 which is concerned with the basics of workflow performance. The text in the episode does try to make it clear that...