An Introduction to Nextflow and nf-core
Channel: SIB - Swiss Institute of Bioinformatics
Date: 2024-04-07

This talk was recorded live during the SIB course “ Reproducible Research and Data Analysis using Nextflow Pipelines” (https://www.sib.swiss/training/course/20211115_NEXTF) which took place online on 15-18 November 2021. The course material can be found on the dedicated course GitHub repository (https://github.com/biocorecrg/SIB_course_nextflow_Nov_2021?tab=readme-ov-file) and course GitHub Page (https://biocorecrg.github.io/SIB_course_nextflow_Nov_2021/docs/ ).

In the first part of the video, Cédric Notredame gives a brief introduction to Nextflow (https://www.nextflow.io/ ), a pipeline language, the reasons it has been developed, how it has been created and how it works compared to alternative tools. Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
In the second part of the video, Jose Espinosa-Carrasco presents nf-core, a community effort to collect a curated set of analysis pipelines using Nextflow. nf-core also provides resources for developers with templates and tools to help validate code and simplify common tasks. Nextflow tower, a web interface to interact with Nextflow is also highlighted in this video.
 
Target audience: This videos is intended for life scientists, bioinformaticians and researchers, willing to know more about Nextflow and to start using it to achieve reproducibility of data analysis.
 
Speakers: Dr. Cedric Notredame and Dr. Jose Espinosa-Carrasco, Comparative Bioinformatics Group, Centre de Regulació Genòmica (CRG)

Reference papers: 
- Di Tommaso, P., Chatzou, M., Floden, E. et al. Nextflow enables reproducible computational workflows. Nat Biotechnol 35, 316–319 (2017). https://doi.org/10.1038/nbt.3820

- Ewels, P.A., Peltzer, A., Fillinger, S. et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol 38, 276–278 (2020). https://doi.org/10.1038/s41587-020-0439-x


Other resources (with URL) mentioned in this talk:  
nf-core : https://nf-co.re/ 
 
Any question about this talk?  

Contact cedric.notredame@crg.eu and/or  joseantonio.espinosa@crg.eu 

 
This video is available under the creative commons license CC-BY-4.0.