Tim Booth

Use the log directive from the start

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From @cmeesters: > the log directive is crucial. There is no rule, using it, no task implementing it. No lookup performed by the participants. > log is its own directive,...

Chapter 4 solution does not work

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@cmeesters reports: > Chapter 4- The DAG: Major Issue: >the solution does not work

From @cmeesters: > Idea: > > I usually prefer using dot - and demonstrate all possible workflow representations. This way, participants > know how to display and copy&paste "their" DAGs...

Motivation for countreads rule

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From @cmeesters > Major Issue: > here it does not pay out to start with a counting reads rule: there is no motivation to do so. It is not necessary...

Bioinformatics concepts and best practise should be more thoroughly addressed

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Comments from @cmeesters on this topic: * fastx is totally outdated, tools like cutadept are meanwhile good replacements. It is ok to use fastx for didactics, though, as participants can...

Several concerns on Ep 11 (new assembly workflow)

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From review by @cmeesters: *Chapter 11 - Designing a new workflow* This Chapter needs a major revision: * the assembly part comes out of the blue and is unrelated to...

Describe global and per-rule requirements

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Suggestion from @cmeesters to add to Chapter 9: > describe the difference between global and per-rule requirements. > A global requirement might be snakemake, the executor plugin, the file system...