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carpentries-incubator / workflows-nextflow

Workflow management with Nextflow and nf-core
https://carpentries-incubator.github.io/workflows-nextflow/
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Explaining the tools-software we are going to use in exercises #57

Closed kerimoff closed 2 months ago

kerimoff commented 2 years ago

Based on the learner feedback we got after the first training it may be a good idea to explain the tools-software we are using in the examples/exercises (e.g. samtools, salmon, multiqc, fastqc etc.) or since it is argued that Nextflow is not only designed for the use of bioinformaticians the examples/exercises should be replaced to use more general tools/software (e.g. bash commands)

I am more in favour of explaining the tools we are using currently in the pipeline. But, also accept that it is a valid argument and should be probably discussed here or via Slack.

mahesh-panchal commented 2 years ago

Related #54

mahesh-panchal commented 2 years ago

What was your setting here? Did it follow from the carpentries genomics workshop or purely stand-alone? I agree it would be a nice enhancement to have a table on what the tools are for reference.

ggrimes commented 2 years ago

Where would be put this material?

kerimoff commented 2 years ago

What was your setting here? Did it follow from the carpentries genomics workshop or purely stand-alone? I agree it would be a nice enhancement to have a table on what the tools are for reference.

Our training was purely stand-alone. But, in my opinion, we should expect the people who are attending this course also from other disciplines than genomics/bioinformatics. I followed my own fork which probably 98% the same with original https://kerimoff.github.io/workflows-nextflow/02-nextflow_scripting/index.html

and the exercise materials here: https://github.com/kerimoff/nf-training

kerimoff commented 2 years ago

Where would be put this material?

I think it should be a :callout in the beginning of exercise/example where we use the tool for the first time. (e.g. describe what salmon is and how it is used in the beginning of Processes episode)

The other option is to explain all of them in the episode 1 very briefly These are the only ones we need to explain IMO:

mahesh-panchal commented 2 years ago

I think it would be nice if we had a domain specific description at the top with a table of the tools and what they do. The first exercise could then be, with a pen and paper, draw how these tools are connected (inspired by a tweet from Tiffany Timbers and Greg Wilson https://twitter.com/TiffanyTimbers/status/1463940276653740043?t=EWjYSgDXbb4UBrKNSB2NMQ&s=19).