Tim Booth

I think the tests I wrote address this issue, so I'm closing it.

I'd agree that Figshare is problematic. I was copying Data Carpentry: https://datacarpentry.org/image-processing/instructor/index.html#data But I think we can do a bit better. I've also noticed that if you download the file...

I could put a copy of the file here on GitHub, but GitHub does not allow .tar.xz files, and the .tar.gz version is just a tad too big. I guess...

I'm not sure what "the background" is here, but it is true that many new users of Snakemake will use lists where they need multiple inputs and outputs, resulting in...

The `log` directive in Snakemake is a special type of output that does not get deleted if a job fails. Outside of failure conditions, both `output` and `log` are treated...

I've now covered the `log:` directive in ep4. I'm not adding a log to every rule later in the course as I feel that reducing clutter is more important here...

I have run through every command in episode 04, using the Snakefile linked at the top of the episode. I can't see any errors. I must be missing something. Can...

A plausible motivation for counting the reads both pre- and post- trimming is to see how many reads get discarded by the trim. But as it stands, we get close...

I implemented something like "Idea 2" with a `calculate_difference` rule to give some closure/justification to the read counting rule. This allows me to keep ep03 more manageable by splitting it...

I have now replaced the `all_counts` rule with an `all_differences` rule that builds on the `calculate_difference`. I think the flow of the lessons is now more satisfactory, and I think...