---
title: nf-core/sarek a Best-Practices community pipeline for WGS/WES
tags: nf-core, sarek, GenPhySE
type: slide
---

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<a href="https://www.nf-co.re/sarek"><img src="https://raw.githubusercontent.com/nf-core/sarek/master/docs/images/logos/nf-core_sarek/nf-core_sarek_dark_color.svg" width="65%"><img></a>

#### A Best-Practices community pipeline for WGS/WES

<small>

Maxime U Garcia ▸ [<i class="fa fa-github"></i>@maxulysse](https://github.com/maxulysse/)
[Seqera Labs](https://seqera.io/) ▸ Barcelona | Stockholm

2023-03-06@[Genphyse](https://genphyse.toulouse.inra.fr/seminars/2023/maxime-garcia)

</small>

---

## 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" width="50%"><img></a>

<font size=5>
<a href="https://doi.org/10.1093/gigascience/giy077">10.1093/gigascience/giy077</a>
</font>

---

## What is Sarek

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A [National Park](https://www.sverigesnationalparker.se/en/choose-park---list/sarek-national-park/) in Northern Sweden.

<small>

* Long, deep, narrow valleys and wild, turbulent water
* A tortuous delta landscape
* Completely lacking in comfortable accommodations
* One of Sweden’s most inaccessible national parks
* There are no roads leading up to the national park

</small>

---

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---

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## Explore strange new worlds

<div class="multi-column">

<div>
<small>

* [Sarek](https://github.com/SciLifeLab/Sarek/releases/tag/2.0.0)
* [Ruotes](https://github.com/SciLifeLab/Sarek/releases/tag/2.1.0)
* [Skårki](https://github.com/SciLifeLab/Sarek/releases/tag/2.2.0)
* [Äpar](https://github.com/SciLifeLab/Sarek/releases/tag/2.3)

</small>
</div>

<div>
<small>

* [Ålkatj](https://github.com/nf-core/sarek/releases/tag/2.5)
* [Årjep-Ålkatjjekna](https://github.com/nf-core/sarek/releases/tag/2.5.1)
* [Jåkkåtjkaskajekna](https://github.com/nf-core/sarek/releases/tag/2.5.2)
* [Piellorieppe](https://github.com/nf-core/sarek/releases/tag/2.6)
* [Gådokgaskatjåhkkå](https://github.com/nf-core/sarek/releases/tag/2.6.1)
* [Pårte](https://github.com/nf-core/sarek/releases/tag/2.7)
* [Pårtejekna](https://github.com/nf-core/sarek/releases/tag/2.7.1)
* [Áhkká](https://github.com/nf-core/sarek/releases/tag/2.7.2)

</small>
</div>

<div>
<small>

* [Skierfe](https://github.com/nf-core/sarek/releases/tag/3.0)
* [Saiva](https://github.com/nf-core/sarek/releases/tag/3.0.1)
* [Lájtávrre](https://github.com/nf-core/sarek/releases/tag/3.0.2)
* [Rapaätno](https://github.com/nf-core/sarek/releases/tag/3.1)
* [Lilla Luleälven](https://github.com/nf-core/sarek/releases/tag/3.1.1)
* [Lesser Lule River](https://github.com/nf-core/sarek/releases/tag/3.1.2)

</small>
</div>

</div>

---

[](https://nf-co.re/sarek)

* Open-Source Nextflow Pipeline
* Community driven

---

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

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

---

## Data driven language

The execution graph depends on the input data,
and is calculated on the go.

In `snakemake`, it's the other way around.

The execution graph depends on the final target,
and is calculated before launch.

---

## Portability

[www.nextflow.io/docs/latest/executor.html](https://www.nextflow.io/docs/latest/executor.html)

* <i class="fa fa-server"></i> Sun Grid Engine, SLURM, PBS/Torque...
* <i class="fa fa-cloud"></i> AWS, Azure, Google...

---

## Reproducibility

<div class="multi-column">

<div>

[ ](https://bioconda.github.io/)

</div>
<div>

[](https://www.docker.com/)

</div>
<div>

[](https://sylabs.io/singularity/)

</div>
</div>

---

[](https://nf-co.re/sarek)

<div class="multi-column">

<div>

<div>Started at</div>

* [NGI](https://ngisweden.scilifelab.se/)
* [NBIS](https://nbis.se/)
* [BTB](https://ki.se/forskning/barntumorbanken)

</div>

<div>

<div>Continued at</div>

* [QBiC](https://www.qbic.uni-tuebingen.de/)
* [DNGC](https://eng.ngc.dk/)
* [GHGA](https://www.ghga.de/)
* [Seqera Labs](https://seqera.io/)

</div>

</div>

---

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## Multiple flavors


<div class="multi-column">

<div>

</div>

<div>

</div>

</div>

---

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## Multiple modes


---

## Reference genomes

* Currently using [AWS iGenomes](https://registry.opendata.aws/aws-igenomes/)
* Considering [refgenie](http://refgenie.databio.org/en/latest/)

---

## Preprocessing

[](https://software.broadinstitute.org/gatk/best-practices/)

Based on GATK Best Practices (GATK 4.3.0.0)

* Reads mapped to reference genome with `bwa mem`
* Duplicates marked with `picard MarkDuplicates`
* Recalibrate with `GATK BaseRecalibrator`

---

## Germline Variant Calling

<small>

* SNVs and small indels
* Deepvariant
* Freebayes
* HaplotypeCaller
* mpileup
* Strelka2
* Structural variants
* Manta
* TIDDIT
* CNVs
* CNVKIT

</small>

---

## Somatic Variant Calling

<small>

* SNVs and small indels
* Freebayes
* Mutect2
* Strelka2
* Structural variants
* Manta
* TIDDIT
* Sample heterogeneity, ploidy and CNVs
* ASCAT
* CNVKIT
* Control-FREEC
* Microsatellite instability
* MSIsensorpro

</small>

---

## Annotation

<small>

* Ensembl-VEP and SnpEff
* ClinVar, COSMIC, dbSNP, GENCODE, gnomAD, polyphen, sift, etc.

</small>

---

## Reports

[](https://multiqc.info/)

---

[](https://github.com/nf-core/sarek/releases/tag/3.1.1)

---

## Sarek in Nextflow Tower

[cloud.tower.nf](https://cloud.tower.nf/)

---

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

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

---

# Community


---

# Users


---

# Developers


---

# What does nf-core provide

* **Pipelines**: ready-made pipelines
* **Docs <i class="fa fa-globe"></i>**: Guidelines, tutorials, videos
* **Modules <i class="fa fa-globe"></i>**: single-tool wrappers
* **Subworkflows <i class="fa fa-globe"></i>**: multi-tool wrappers
* **Configs <i class="fa fa-globe"></i>**: shared infrastructure configs
* **Test datasets <i class="fa fa-globe"></i>**: test data for :point_up_2:
* **Tools <i class="fa fa-globe"></i>**: linting, template + automation for :point_up_2:

---

## Pipeline requirements

[<i class="fa fa-globe"></i> nf-co.re/docs/contributing/adding_pipelines](https://nf-co.re/docs/contributing/adding_pipelines)

* Nextflow based
* Common structure
* Stable release tags
* MIT license
* Software bundled for reproducibility
* Continuous Integration testing
* _lagom_

---

## <i class="fa fa-laptop"></i> Training and other events

[<i class="fa fa-globe"></i> https://nf-co.re/events](https://nf-co.re/events)

<a href="https://nf-co.re/events/2020/hackathon-francis-crick-2020"><img src="https://maxulysse.github.io/assets/img/slides/nf-core_hackathon_crick2020.jpg" width="60%"><img></a>

<small>

* [<i class="fa fa-globe"></i> nf-co.re/events/2023/training-march-2023](https://nf-co.re/events/2023/training-march-2023)
* [<i class="fa fa-globe"></i> nf-co.re/events/2023/hackathon-march-2023](https://nf-co.re/events/2023/hackathon-march-2023)

</small>

---

## Need help?

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

Website: [`https://nf-co.re`](https://nf-co.re)
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