<section data-background-image="https://maxulysse.github.io/assets/img/background/Sarek-Park-02.jpg" data-background-opacity=0.5 > # Bioinformatics ## updates Maxime Garcia <small> [<i class="fab fa-twitter"></i> @gau](https://twitter.com/gau) [<i class="fab fa-github"></i> @MaxUlysse](https://github.com/MaxUlysse) [virtual] - 2020/10/22 </small> --- [](https://nf-co.re/sarek) <!-- .element class="image-H10" --> * Detect germline and somatic variants (WGS/WES) * Open-Source Nextflow Pipeline * Started at NGI * In collaboration with NBIS * Support from BTB * In collaboration with QBiC (Tübingen) --- ## Publication in F1000Research Sarek: A portable workflow for whole-genome sequencing</br> analysis of germline and somatic variants</br> [version 2; peer review: 2 approved] <small> Maxime Garcia, Szilveszter Juhos, Malin Larsson, Pall I. Olason, Marcel Martin,</br> Jesper Eisfeldt, Sebastian DiLorenzo, Johanna Sandgren, Teresita Díaz De Ståhl,</br> Philip Ewels, Valtteri Wirta, Monica Nistér, Max Käller, Björn Nystedt </small> [<i class="ai ai-doi"></i> doi.org/10.12688/f1000research.16665.2](https://doi.org/10.12688/f1000research.16665.2) --- ## What is coming soon * DSL 2 ([dsl2](https://github.com/nf-core/sarek/tree/dsl2)) with [Gisela Gabernet](https://github.com/ggabernet), [Friederike Hanssen](https://github.com/FriederikeHanssen), [Harshil Patel](https://github.com/drpatelh) and [Phil Ewels](https://github.com/ewels) * Code fully modular * Atomic containers * More tools * Sub-workflows for specific usage * Improved cloud usage * Validation tests * More downstream processing of the final vcf files --- [](https://nf-co.re/rnafusion) <!-- .element class="image-H10" --> <div class="fragment fade-in" data-fragment-index="2"> * Open-Source Nextflow Pipeline * Part of nf-core * Started at NGI * Support from BTB </div> <div class="fragment fade-in" data-fragment-index="3"> <small> Project initiated by [Rickard Hammarén](https://github.com/Hammarn), fully matured under [Martin Proks](https://github.com/matq007), shamelessly taken over by me. </small> --- ## What is coming next * DSL 2 * More tools * Easier configuration --- [](https://nf-co.re) <!-- .element class="image-H10" --> Publication in Nat Biotechnology: The nf-core framework for community-curated</br> bioinformatics pipelines [<i class="ai ai-doi"></i> 10.1038/s41587-020-0439-x](https://doi.org/10.1038/s41587-020-0439-x) --- ## Hackathons * London (February) [partly online] * Heidelberg (July) [online] --- <div class="r-stack"> <img src="/assets/img/svg/acknowledgments_2020.svg" title="Acknowledgements" alt="Acknowledgements" class="image-75 fragment fade-out" data-fragment-index="0"/> <img src="/assets/img/svg/institutes_2020.svg" title="Acknowledgements" alt="Acknowledgements" class="image-75 fragment fade-in-then-out" data-fragment-index="0"/> <img src="/assets/img/slides/nf-core_contributors_jobim.png" title="Acknowledgements" alt="Acknowledgements" class="image-75 fragment fade-in-then-out" data-fragment-index="1"/> <img src="/assets/img/slides/nf-core_sarek_contributors_2.6.1.png" title="Acknowledgements" alt="Acknowledgements" class="image-75 fragment fade-in-then-out" data-fragment-index="2"/> <img src="/assets/img/slides/nf-core_rnafusion_contributors_1.2.0.png" title="Acknowledgements" alt="Acknowledgements" class="image-75 fragment fade-in-then-out" data-fragment-index="3"/> </div> --- <section data-background-image="https://maxulysse.github.io/assets/img/background/Stockholm-by-night.jpg" data-background-opacity=0.5 > ## Any questions * [<i class="fa fa-globe-europe"></i> nf-co.re](https://nf-co.re) * [<i class="fab fa-github"></i> github.com/nf-core](https://github.com/nf-core) * [<i class="fab fa-slack"></i> nfcore.slack.com](https://nfcore.slack.com/) * [<i class="fa fa-globe-europe"></i> nf-co.re/sarek](https://nf-co.re/sarek) * [<i class="fab fa-github"></i> github.com/nf-core/sarek](https://github.com/nf-core/sarek) * [<i class="fab fa-slack"></i> nfcore.slack.com/channels/sarek](https://nfcore.slack.com/channels/sarek) * [<i class="fa fa-globe-europe"></i> nf-co.re/rnafusion](https://nf-co.re/rnafusion) * [<i class="fab fa-github"></i> github.com/nf-core/rnafusion](https://github.com/nf-core/rnafusion) * [<i class="fab fa-slack"></i> nfcore.slack.com/channels/rnafusion](https://nfcore.slack.com/channels/rnafusion)