Week 15: Running nf-core pipelines
1 Overview
This week, we will mainly cover how you can run a bioinformatics pipeline written in the Nextflow language and developed as part of the nf-core initiative. That will take up the Tuesday meeting and part of Thursday’s. On Thursday, we will also have a brief course recap and Q&A session.
2 Learning goals
Specifically, you will learn:
Lecture A: Running nf-core pipelines
- Why you may want to use pipelines like those made by the nf-core initiative
- What the nf-core rnaseq pipeline does, and when you would want to use it
- How these pipelines can be run with a single command, while they submit jobs to the Slurm scheduler at OSC.
- The difference between general Nextflow options and pipeline-specific options when running such a pipeline.
- How to set up inputs and outputs for such a pipeline, including the distinction between a final output dir and a “work dir”.
- How to monitor pipeline progress
- How to restart a pipeline run using the
-resumeoption - How to find and interpret the output files produced by the pipeline
Lecture B: Course recap
- An overview of the topics covered in this course
- Answers to any remaining questions you may have
3 Readings
- Ewels et al. (2020): “The nf-core framework for community-curated bioinformatics pipelines”
4 Further resources
- Di Tommaso et al. (2017): “Nextflow enables reproducible computational workflows”
References
Di Tommaso, Paolo, Maria Chatzou, Evan W. Floden, Pablo Prieto Barja, Emilio Palumbo, and Cedric Notredame. 2017. “Nextflow enables reproducible computational workflows.” Nature Biotechnology 35 (4): 316–19. https://doi.org/10.1038/nbt.3820.
Ewels, Philip A., Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso, and Sven Nahnsen. 2020. “The Nf-Core Framework for Community-Curated Bioinformatics Pipelines.” Nature Biotechnology 38 (3): 276–78. https://doi.org/10.1038/s41587-020-0439-x.