---
title: nf-core presentation
tags: open-source, talk, nf-core
---

<!-- .slide: data-background="https://raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg" -->

<a href="https://nf-co.re"><img src="https://raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-darkbg.svg" width="60%"></img></a>

# What is nf-core\?

[Maxime U Garcia](https://maxulysse.github.io/) ▸ [<i class="fa fa-twitter" aria-hidden="true"></i>@gau](https://twitter.com/gau/) | [<i class="fa fa-github" aria-hidden="true"></i>@maxulysse](https://github.com/maxulysse/)
[Karolinska Institutet](https://ki.se/) | [Science for Life Laboratory](https://www.scilifelab.se/)
Sweden

---

## Overview

- 🗄️ [Barntumörbanken](https://ki.se/forskning/barntumorbanken/)
- 🧬 [NGI](https://ngisweden.scilifelab.se/)
- 🍬 [Nextflow](https://www.nextflow.io/)
- 🧙 [nf-core](https://nf-co.re/)

---

## Reproducibility is central

<a href="https://academic.oup.com/view-large/figure/118918033/giy077fig1.jpg"><img src="https://maxulysse.github.io/assets/img/slides/gigascience_giy077_fig1.jpg" alt="Figure 1" width="50%"></img></a>

[<i class="ai ai-doi"></i> 10.1093/gigascience/giy077](https://doi.org/10.1093/gigascience/giy077)

---

## [Barntumörbanken](https://ki.se/forskning/barntumorbanken/)

_a.k.a._ The Swedish Childhood Tumor Biobank

- Collect pediatric solid tumors samples (+ blood)
- 6 Swedish University Hospitals
- Store samples
- ~ 20 000

---

## National research resource

Pediatric cancer samples and genomic data

- Share samples
- Analyse and share data

---

## [NGI](https://ngisweden.scilifelab.se/)

_a.k.a._ National Genomics Infrastructure

- State-of-the-art infrastructure
- Sequencing (DNA, RNA ...)
- Guidelines and support
- Sample collection, study design, protocol selection
- Bioinformatics analysis

---

## [Nextflow](https://www.nextflow.io/)

* Workflow manager
* Data driven language
* Portable
* executable on multiple platforms
* Shareable and reproducible
* with containers or virtual environments

---

<a href="https://nf-co.re"><img src="https://raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-darkbg.svg" width="60%"></img></a>

---

### [Quick history](https://nf-co.re/about)

- [NGI](https://ngisweden.scilifelab.se/) had been developing analysis pipelines for years and using a set of standards
- This helped other group run the pipelines on their own
- Pipelines began to outgrow the `SciLifeLab/NGI` branding
- In late 2017,` nf-core` was created, thanks to Phil Ewels ([NGI](https://ngisweden.scilifelab.se/)), Alex Peltzer ([QBiC](https://portal.qbic.uni-tuebingen.de/portal/)), Sven Fillinger ([QBiC](https://portal.qbic.uni-tuebingen.de/portal/)) and Andreas Wilm ([A*STAR](https://www.a-star.edu.sg/))
- All relevant pipelines were moved to this new [GitHub organisation](https://github.com/nf-core)

---

### Join the [community](https://nf-co.re/community/)

- [GitHub](https://github.com/nf-core)
- [Slack](https://nf-co.re/join/slack)
- [Twitter](https://twitter.com/nf_core)
- [YouTube](https://www.youtube.com/c/nf-core)
- [Hackathons](https://nf-co.re/events/2022/hackathon-march-2022)

---

### What we want in our pipelines

- [Nextflow](https://www.nextflow.io/) based
- Common structure (based on our nf-core template)
- Stable release tags
- MIT license (can be used even in commercial settings)
- Using [biocontainers](https://biocontainers.pro/) (if possible)
- Continuous Integration testing ([GitHub Actions](https://github.com/features/actions))
- One pipeline per data type/usage ([lagom](https://www.atlasobscura.com/places/the-lagom-standard-measure))

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### [Pipelines availability](https://nf-co.re/pipelines)

- Our website has pages for each pipeline that renders the documentation available on GitHub
- 33 released pipelines
- 27 in development

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### [A companion tool](https://nf-co.re/tools)

- [nf-core launch](https://nf-co.re/tools#launch-a-pipeline) - Run pipeline with interactive prompts
- [nf-core download](https://nf-co.re/tools#downloading-pipelines-for-offline-use) - Download pipeline for offline use
- [nf-core create](https://nf-co.re/tools#creating-a-new-workflow) - Create a new pipeline from the template
- [nf-core lint](https://nf-co.re/tools#linting-a-workflow) - Check pipeline code against guidelines
- [nf-core modules](https://nf-co.re/tools/#modules) - Commands for dealing with DSL2 modules

---

### Configurations

All pipelines come with a default sensible configuration for a regular sized HPC

[nf-core/configs](https://github.com/nf-core/configs/) allows shared configurations between pipelines for a specific HPC

* cpus, time and memory requirements
* scheduler
* queues
* environments
* path to common references files

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### [Modules](https://nf-co.re/modules)

Modules are the building stones of all DSL2 nf-core blocks.
Can be used outside nf-core as well.

---

### Demo

# Install Nextflow
curl -s https://get.nextflow.io | bash

# Run a nf-core pipeline with test data
nextflow run nf-core/sarek -r dev -profile test,docker

---

## Acknowledgements

<img src="https://raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/acknowledgments_2021_dark.svg" title="Institutes acknowledgements" alt="Institutes acknowledgements"/>

---

<a href="https://nf-co.re/community#organisations">
<img src="https://raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/institutes_2021_dark.svg" title="Institutes acknowledgements" alt="Institutes acknowledgements"/>
</a>

---

<a href="https://nf-co.re/community#contributors">
<img src="https://raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/slides/nf-core_contributors_2021_03.png" title="Contributors acknowledgements" alt="Contributors acknowledgements"/>
</a>

---

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## Any questions?

Get involved:
[https://nf-co.re/join](https://nf-co.re/join)

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