workflows-nextflow

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Could this detail be referred to rather than included? Perhaps it is enough to say it's a unique ID? https://carpentries-incubator.github.io/workflows-nextflow/08-reporting.html#task-id

ggrimes

There's a lot of really good content in this episode, but will all of it be relevant to new Nextflow users? https://carpentries-incubator.github.io/workflows-nextflow/07-operators.html#grouping-contents-of-a-channel-by-a-key- might be a bit complicated? Or perhaps this...

ggrimes

Is it safe to assume that learners will be familiar with regular expressions? If not https://carpentries-incubator.github.io/workflows-nextflow/07-operators.html#regular-expression may be confusing.

ggrimes

I get an error when running the first code block: This persists with subsequent examples ``` executor > local (10) [e5/e6fded] process > FASTQC (5) [100%] 9 of 9 ✔...

ggrimes

Nextflow review @bobturneruk ep4 ${...}

1

Do inputs need to be wrapped in ${...} when used in a script? What is good practise?

ggrimes

Nextflow review @bobturneruk ep5 , CPUs, cores and threads

1

Is it worth making the difference between CPUs, cores and threads clear here? https://carpentries-incubator.github.io/workflows-nextflow/05-processes-part2.html#directives

ggrimes

The work directory is mentioned here for the first time, but not explained until ep10. It might be good to offer a very brief explanation of it at this point?

ggrimes

Is it necessary to introduce this alternative shell: way of using Bash in Nextflow, please? Perhaps better to stick with script:? https://carpentries-incubator.github.io/workflows-nextflow/04-processes-part1.html#shell

ggrimes

I suspect this would be a difficult thing to do, but perhaps the Python and R material should be removed in the interests of time?

ggrimes

Nextflow review @bobturneruk ep4 python/Rscript script

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- Could `PYSTUFF `be called something more specific, please? Same for `RSTUFF.` It's better for readers if short, descriptive names are used. - Could `myscript.py` be called something more specific,...

ggrimes