Tim Booth
Tim Booth
From @jdblischak You have the learners write the output field before the input field. And your motivation is that it is natural to work backwards when writing a Snakefile, eg:...
In general the episodes are longer than the Carpentries recommendation, and especially episode 6 is very long. Probably some of the more detailed stuff in the first part (FastQC) can...
Comment from Ezra: > Lesson “Cleaning up” – protected files. I’ve never used this functionality before and found it difficult to explain why it would be useful, as it stops...
From @cmeesters: > Kallisto performs (wording according to docs) a "pseuoalignment" - it is not a classical aligner and should > not be mentioned as such. > "If you know...
from @cmeesters: > we recommend using Snakemake wrapper to handle awkward programs to increase the stability of workflows > wherever possible. There is not even an outlook to wrappers. This...
From @cmeesters: > A pretty good chapter. Yet, now there cannot be a one-file solution. You ask participants to > download the solution and split the content into different files...
Suggestion from @cmeesters, in Ep05 "Processing Lists of Inputs": > Personally, as a teacher, I would very much prefer to split this into tiny tasks and have a solution for...
From @cmeesters: > Chapter 7 - Finishing > Again, a nice description. The solution, however, does not work, > and stating in the file # "rule all_counts" has been removed...
From @cmeesters: > "See this link for details about this dataset and the redistribution licence." contains the link > https://figshare.com/articles/dataset/data-for-snakemake-novice-bioinformatics_tar_xz/19733338/1. > It leads to a description on summary level, but...
From @cmeesters: > [in ep03] we get to named in- and output without explaining the background or that in- and output are usually lists.