A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Can someone point me to documentation for adding a step to a pipeline? Specifically, I want to add a samtools index step so that both BAM and BAI files are output from the scrnaseq pipeline.

Is this what you mean? <https://training.nextflow.io/latest/hello_nextflow/03_hello_workflow/#1-add-a-second-step-to-the-workflow>
Or do you need something else?

This describes finding a module: <https://training.nextflow.io/latest/hello_nf-core/03_use_module/#11-browse-available-modules-on-the-nf-core-website>

At the top of the Documentation landing page there is also this if you want nf-core specific docs (it's a bit out of date though, missing nf-test info if <#CHN5BV5DW|> has implemented that)

<https://nf-co.re/docs/tutorials/nf-core_components/adding_modules_to_pipelines|https://nf-co.re/docs/tutorials/nf-core_components/adding_modules_to_pipelines>

Wonderful, thank you both! It looks like this is the info I needed.