Materials for nf-core preh-hackathon training KEMRI-wellcome Trust Program site
| Date/Time | Topic |
|---|---|
| Mar 03, 4:00pm - 5:00pm | Introduction to nextflow |
| Mar 05, 3:00pm - 4:30pm | Channels and processes |
| Mar 10, 4:00pm - 5:00pm | Workflow and operators |
| Mar 12, 3:00pm - 4:00pm | Reporting and config files |
| Mar 17, 4:00pm - 5:00pm | Worflow caching and checkpointing |
| Mar 19, 3:00pm - 4:00pm | Hands on: A simple nextflow pipeline |
- what a workflow management system is.
- The benefits of using a workflow management system.
- Explain the benefits of using Nextflow as part of your bioinformatics workflow.
- Explain the components of a Nextflow script.
- How to install nextflow
- Run a Nextflow script.
Please have the following software and user accounts ready.
- GitHub Account
- Docker Hub Account
- Visual Studio Code or your favorite code editor.
A preconfigured Nextflow development environment is available using Gitpod. To run Gitpod:
- Click the following URL: https://gitpod.io/#https://github.com/nextflow-io/training -- This is nextflows GitHub repository URL, prefixed with https://gitpod.io/#
- Log in to your GitHub account (and allow authorization).
- Once you have signed in, Gitpod should load (skip prebuild if asked).
- If you decided to use the Gitpod environment, you don`t need to install anything into your local computer! But still, you would need to have github and docker accounts
To follow the training on your computer, you will need the following software and files:
- Bash
- Java11 (or later, up to 18)
- Nextflow
- nf-core
- nf-core tools on Github
- Docker
- GitHub CLI
- Data
- https://www.ghga.de/
- https://carpentries-incubator.github.io/workflows-nextflow/01-getting-started-with-nextflow.html
Documentation and reference material for nextflow:
- Nextflow homepage: https://www.nextflow.io/
- Nextflow training material: https://training.nextflow.io
- Pipeline examples: https://www.nextflow.io/example1.html
- Main documentation: https://www.nextflow.io/docs/latest/index.html
- Common implementation patterns for developers: http://nextflow-io.github.io/patterns/index.html
Docker for beginners:
Github Actions & GitHub CI:
- https://docs.github.com/en/actions/automating-builds-and-tests/about-continuous-integration
- https://resources.github.com/ci-cd/
Do you have any questions? mail to oyesigyemukamaadolf25@gmail.com
- Firas Zemzem : PhD student ,Laboratory of Cytogenetics, Molecular Genetics and Biology of Reproduction CHU Farhat Hached Sousse, Higher institute of Biotechnology of Monastir, University of Monastir, Tunisia