<!-- .slide: data-background-color="white" -->
### Future possibilities for collaboration
| <a href="https://www.icgc-argo.org/"><img src="https://icgcargo.blob.core.windows.net/assets/uploads/img/masterpage/logo-header.png" height="120px"><img></a> | <a href="https://www.nf-co.re/"><img src="https://raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo.svg" height="120px"><img></a> |
| :-: | :-: |
<p style="color:black;">
Maxime U Garcia ▸ <i class="fa fa-github first_page" aria-hidden="true"></i> <a href="https://github.com/maxulysse/">@maxulysse</a>
</p>
<p style="color:black;">
Scientific Development @ <a href="https://seqera.io/">Seqera Labs</a>
</p>
---
## Overview
- 🍏 What is `nf-core`?
- 🧙 What can be done with `nf-core`?
- 🚀 How to use `nf-core` outside `nf-core`?
---
## Reproducibility
<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" height="400px"><img></a>
[doi: 10.1093/gigascience/giy077](https://doi.org/10.1093/gigascience/giy077)
---
## How it started
- Late 2017
- [NGI](https://ngisweden.scilifelab.se/) | Sweden
- [QBiC](https://portal.qbic.uni-tuebingen.de/portal/) | Germany
- [A*STAR](https://www.a-star.edu.sg/) | Singapore
- Plan to develop pipelines conjointly
- Based on [NGI Nextflow pipelines](https://github.com/orgs/SciLifeLab/repositories?q=NGI&type=archived)
---
### High quality pipelines
- [<i class="fa fa-globe" aria-hidden="true"></i> nf-co.re/pipelines](https://nf-co.re/pipelines) (41 ✅ + 25 ⚙️ + 6 🗃️):
- [Requirements](https://nf-co.re/docs/contributing/guidelines#requirements)
- 1 pipeline per data/analysis type
---
## Shared template
- [Base squeleton to create pipelines](https://github.com/nf-core/tools/tree/master/nf_core/pipeline-template)
- Regularly synced
- Centralized [documentation](https://nf-co.re/)
- Auto-generated for `--params`
- Sensible default resources requirements
- Shared [nf-core/configs](https://github.com/nf-core/configs/)
- Continuous Integration with GitHub Actions
- Releases tested on AWS
- Microsoft Azure is coming
---
### Code - Community driven/reviewed
- [<i class="fa fa-globe" aria-hidden="true"></i> nf-co.re/tools](https://nf-co.re/tools/):
- Linting + Template + Common tasks
- [<i class="fa fa-globe" aria-hidden="true"></i> nf-co.re/modules](https://nf-co.re/modules) (707):
- Single unit of building block
- Containers from [BioContainers](https://biocontainers.pro/)
- [<i class="fa fa-globe" aria-hidden="true"></i> modules/subworkflows](https://github.com/nf-core/modules/tree/master/subworkflows/nf-core) (25):
- Modules chained into common goal
---
## Community
- GitHub (525): [<i class="fa fa-globe" aria-hidden="true"></i> github.com/nf-core](https://github.com/nf-core)
- Slack (4153): [<i class="fa fa-globe" aria-hidden="true"></i> nf-co.re/join/slack](https://nf-co.re/join/slack)
- nf-core/bytesize (53): [<i class="fa fa-globe" aria-hidden="true"></i> youtube.com/nf-core](https://www.youtube.com/playlist?list=PL3xpfTVZLcNiSvvPWORbO32S1WDJqKp1e)
- nf-core/hackathon (10): [<i class="fa fa-globe" aria-hidden="true"></i> nf-co.re/events](https://nf-co.re/events/2023/hackathon-march-2023)
- Training (2): [<i class="fa fa-globe" aria-hidden="true"></i> youtube.com/nf-core](https://www.youtube.com/playlist?list=PL3xpfTVZLcNiqYQ41g0fvyTQazpafFvOn)
---
## Examples
- [module/bwa_mem](https://nf-co.re/modules/bwa_mem)
- [subworkflow/fastq_align_bwa](https://github.com/nf-core/modules/tree/master/subworkflows/nf-core/fastq_align_bwa)
- nf-core/pipeline: [nf-core/sarek](https://github.com/nf-core/sarek/) - [Nextflow summit's talk](https://www.youtube.com/watch?v=m9IH8VHUl0g)
- pipeline built using nf-core: [Bactopia](https://bactopia.github.io/latest/) - [Nextflow summit's talk](https://www.youtube.com/watch?v=I0z1z7EKv2M)
---
## 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>
---
<!-- .slide: data-background="https://raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg" -->
More infos:
- [Creating a new pipeline](https://nf-co.re/tools/#creating-a-new-pipeline)
- [Customizing the creation of a pipeline](https://nf-co.re/tools/#customizing-the-creation-of-a-pipeline)
- [Contributing to a module](https://nf-co.re/docs/contributing/modules)
- [Contributing to a subworkflow](https://nf-co.re/docs/contributing/subworkflows)
Get involved:
[https://nf-co.re/join](https://nf-co.re/join)
[<img src="https://nf-co.re/assets/img/slack.svg" class="join">](https://nfcore.slack.com/) | [<img src="https://nf-co.re/assets/img/github.svg" class="join">](https://github.com/nf-core)| [<img src="https://nf-co.re/assets/img/youtube.svg" class="join">](https://www.youtube.com/c/nf-core)
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