---
# System prepended metadata

title: nf-core developer beginner tutorial - initial notes
tags: [' training', documentation]

---


Who? @FriederikeHanssen and @FranBonath 

# Description
A tutorial that takes beginners after the initial Nextflow tutorial and introduces them to the nf-core template and how to make a first basic nf-core pipeline. It should also include some kind of trouble shooting advise.

A first outline was created by Rike for a on-site tutorial, which was as follows:
1. Create a pipeline from the template
- FastQC & MultiQC already installed
2. Test your pipeline
3. Expand with an nf-core/modules module:
- Install bwa/index & bwa/mem
- Add both modules to the pipeline
4. Expand with a subworkflow:
- Install Picard Markduplicates subworkflow
- Install module: samtools/faidx
5. Patch a module
6. Collect versions
7. Test your pipeline

## Existing Material

- ISMB Tutorial:
    - https://docs.google.com/presentation/d/1DaA84FgKVxG6BjkSVAzIKURPMMNQ53NP1xfzakPeX44/edit?usp=sharing
- Elixir Tutorial
    - https://docs.google.com/presentation/d/1-RJukMO_PXUtKfcLFB1-Qxy_rz84kBSZSZWpXvfO2UY/edit?usp=sharing
- https://nf-co.re/docs/contributing/tutorials/adding_modules_to_pipelines
- I like the "tips and tricks" section here
    - https://nf-co.re/docs/usage/introduction
- probably too advanced for this, but if the pipeline is added to the nf-core repo
    - https://nf-co.re/docs/contributing/adding_pipelines
- Instructions if a pipeline is not going to be an official nf-core pipeline (only shows what needs to be amended from the nf-core template)
    - https://nf-co.re/docs/contributing/tutorials/unofficial_pipelines
- Found it! (It's not linked in docs), it even has a gitpod!
    - https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core#creating-a-pipeline

- Suggestion: Take the "Simple RNAseq workflow" from the Nextflow beginners training and make this in an example nf-core pipeline. This may show the difference and similarities between nextflow and nf-core type pipelines.


## Pre-requisits
- knowledge of the comand line 
- Nextflow basic training
- very basic github

## Technical issues

- Keep it in the nextflow repository or move it to he nf-core page?
~~- If we keep it in the nextflow repository:
    - The repo currently contains the basic training and advanced training. However, the code structure is a bit awkward at the moment and users need to navigate around a lot. We could this opportunity to separate out the trainings into multiple gitpod spaces. ~~
    - We decided to keep it on the nf-core website for now. Issues may still be:
        - Users need to check multiple places
        - we need to work out how to set things up on our side

- 



## BIG To Do's
- make a final outline of the course content
- create a course repo
- write the documentational text around the course
- define proper hands on excercises and integrate them in the course
- create a gitpod environment
- Test the course