Suggestion: Limit RNAseq tools to a single episode

[mahesh-panchal]

One suggestion that may help with uptake is to limit the RNAseq workflow tools and scripts to a single episode.

@sateeshperi would like to use a variant calling workflow instead for his episodes. This could be included here then as a supplementary episode which could be a drop-in replacement for the RNAseq workflow scripting episode.

It would also allow us to incorporate other domain specific workflow episodes such as for image analysis, proteomics, etc so teachers can deliver this course more easily to their domain.

This may also then help with environment setup if the scripts are then changed to only use bash commands, such that only nextflow, java, and nf-core are necessary requirements. Each domain specific episode could have it's own conda/package manager environment setup too.

[sateeshperi]

Thats right @mahesh-panchal....it would be great to have a drop-down box somehow to let users choose the workflow they would be interested in. Here is the link to variant-calling tutorial

[sateeshperi]

one way to limit chapters to episodes would be to use nf-core to create domain-specific pipelines. For example, this is a single episode to assemble variant-calling pipeline using nf-core modules (still work in progress!)

[mahesh-panchal]

It would be good to have a list of domain specific pipelines to include and what they do. Perhaps that could be the landing page (episode 9) and then it links out to the supplementary episodes for each domain. We start out with these two.

• RNAseq
• Variant Calling.

[sateeshperi]

need to think this through......in the current carpentries lesson layout nf-core is not introduced until chapter-15

[mahesh-panchal]

Met up at the nf-core hackathon for some discussion.

Summary:

• Need to check for a more generalized data set (Is https://swcarpentry.github.io/shell-novice/02-filedir/index.html suitable?), otherwise we stick to using the yeast data set.
• Earlier episodes should be changed to use general shell commands.
• nf-core material should only introduce nf-core and show how to customize and run a workflow.
• An additional episode ( or just an exercise ) to compose a workflow using nf-core modules.
• Adapt episode 1 from https://sateeshperi.github.io/nextflow_varcal/nextflow/ to here.