Nfcore intermediate training

[FriederikeHanssen]

This training covers:

• how to create a pipeline with a stripped down template version
• how to add an existing nf-core module
• a brief explanation of meta maps and how to add new fields from the samplesheet
• how to create a custom module and add it in

This training does not cover:

• Igenomes
• Install and use subworkflows
• How to update components
• Anything related to GitHub actions, CI/CD, (nf-test) testing (aside from -profile test), etc.
• Devcontainers (gitPod, Codespaces)
• How to add more files to MultiQC
• Mulled containers / Seqera containers
• Different resource labels
• Linting
• Bigger samplesheet adaptations
• Elaborate meta map access with closures, i.e. in the modules.config
• Stub tests
• All ext. fields in the modules.config
• Git branches
• How to create your own test profile or where it is stored
• Patching of modules

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[pinin4fjords]

A few more minor things, think this works well for now.

Possibly, after next week's training, rather than fairly disjointed examples, we can start to apply a bit more more narrative to this. So, "we want to build a pipeline to do x, here's how we do that using nf-core tooling and resources"

[FriederikeHanssen]

Possibly, after next week's training, rather than fairly disjointed examples, we can start to apply a bit more more narrative to this. So, "we want to build a pipeline to do x, here's how we do that using nf-core tooling and resources"

agreed!

[christopher-hakkaart]

Some minor language suggestions and typos. Please double check the commands haven't changed. E.g., nextflow pipelines schema build not nextflow schema build

[christopher-hakkaart]

I've added a bunch of minor comments. Most of the are language suggestions. I don't see any major blockers so I've approved.

[adamrtalbot]

I really like this module! I'd say it's a little long, but I don't feel like time is our biggest concern and it's a great introduction to nf-core.

Most of my comments are just refinements on the language or examples which could be updated, nothing too serious.