First pass of the Nextflow Run course

[vdauwera]

Course outline

• Run basic operations (Hello World level)
• Run pipelines (channels for multiple inputs, multi-step example, modules, containers)
• Configuration

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planned for later

• Run nf-core pipelines (for now we can simply jump to the first section of hello nf-core)
• Run with Seqera (with tower, platform, AI)

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[mribeirodantas]

Commands that would be interesting to have in the Nextflow Run training in more detail:

For a shorter Nextflow Run:

• nextflow pull
• nextflow list
• nextflow view
• nextflow inspect
• nextflow run
• nextflow clean
• nextflow log
• nextflow config

In case we don't mind length:

• nextflow lineage
• nextflow secrets
• nextflow plugin

[mribeirodantas]

I committed a few minor fixes and left some comments/suggestions.

[vdauwera]

I committed a few minor fixes and left some comments/suggestions.

Thank you so much! Really appreciate it. Will address the remaining comments (might be tomorrow).

[kenibrewer]

I'll do a review today too while I'm on my flight.

[kenibrewer]

Looks really good to me. I have some suggestions on the config chapter. My main suggestion is teaching the pattern of running nextflow pipelines in a different work directory than where your code is located. Otherwise this looks great and good-to-go.

I addressed Marcel's comments and Ken is on deck, so no need for Marcel to re-review on a Saturday

[kenibrewer]

Lgtm!

[vdauwera]

All done