pre-hackathon_training

Materials for nf-core preh-hackathon training KEMRI-wellcome Trust Program site

Schedule

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

• Meeting Link

Day 01

Learning Objectives

• 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.

Practical Session

• Ensure that you've conda installed. Incase you don't you can follow these steps First navigate to your home directory

cd ~ 
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

Then run the command below. Type yes for all the prompts

bash Miniforge3-$(uname)-$(uname -m).sh

Then restart your terminal

source ~/.bashrc

Create a conda environment and install nextflow in that env

conda create -n nextflow bioconda::nextflow

Overview for today's practical session

We shalll create a small pipeline that performs quality control on sequencing reads using FastQC and fastp, generates a summary report using MultiQC, and assembles the genome using shovill.

Initially, we will write the pipeline as a single script and later modularize it.

We shall use 2 paired end sequences of Sars-cov2 as our test data

Key parts of the pipeline include;

• Defining parameters to parse our test data into the pipeline
• defining processes for fastqc, fastp, multiqc and shovill.
• Creating a workflow
• creating a config file

Requirements

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

Resources

• 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:

• https://docker-curriculum.com/

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 [email protected]

Contributors :

• 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