#BGA23/sessions#Pipeline#Nextflow#NF-Core#Workshop
This session may now be out of date so beware!!!
This session is part of BGA23
Session Leader(s)
Solenne Correard, Resarch associate for the Canada Biogenome Project
I would like to acknowledge that I am living and working on the traditional, ancestral, and unceded territory of the Musqueam, Squamish and Tsleil-Waututh people.
Affiliation : Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre
I did my PhD in France studying the dog genome (mostly the non-coding part), followed by a post-doc on the Silent Genomes Project, a project aiming to reduce health care disparities and improve diagnostic success for children with rare genetic diseases from Indigenous populations in Canada. I am now leading the bioinformatic analysis for the Canadian BioGenome Project.
Description
GitHub:: https://github.com/BGAcademy23/nextflow-genomics
The session will last for about 1h30, and will be split in 2 parts of about 40 min each (we’ll take a 10 min break in the middle).
Each part will include an introduction, some coding and hopefully many questions and discussion!
Outline of the session :
- Nextflow (Part 1) : What is it? When should I use it? How do I use it?
Practice : Writing your first Nextflow pipeline to generate a contig assembly.
- NF-core (Part 2): What is it? When should I use it? How do I use it?
Practice : Use NF-core tools to assess the quality of the generated assembly.
- Conclusion: Resources to learn more about Nextflow and NF-core and how to take part in the community.
By the end of this session you will be able to:
- Read a nextflow pipeline and modify it
- Write a basic nextflow pipeline
- Use a nf-core pipeline
- How to join the nextflow / nf-core community
The outline may change if I come up with a better idea while generating the material!
Prerequisites
- Expertise with linux command line basics (
cd,mv,rm,wget,curletc) - Understanding of bash scripts, and the need for bioinformatics workflows
- Understand the general role and input/output files of the following tools : hifiasm HiFi only, Quast, multiQC
!!! warning "Please make sure you MEET THE PREREQUISITES and READ THE DESCRIPTION above"
You will get the most out of this session if you meet the prerequisites above.
Please also read the description carefully to see if this session is relevant to you.
If you don’t meet the prerequisites or change your mind based on the description or are no longer available at the session time, please email tol-training at sanger.ac.uk to cancel your slot so that someone else on the waitlist might attend.