Advanced Training: Developing Workflows 2023 (Introductory)

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Introductory Stream

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Intended audience:

Beginner - intermediate level bioinformaticians working with next-generation sequencing data for disease surveillance on the African continent

Purpose:

High-throughput laboratory machines generate large quantities of primary biological data. Processing these data to generate useful information involves several tools and setting up of complex bioinformatics environments across heterogeneous computing infrastructure. Bioinformatics workflow managers provide portability and reproducibility of analysis and optimization of available computing resources.

The Advanced Bioinformatics workflow workshop was aimed at introducing and deploying Nextflow, a tool that enables scalable and reproducible scientific workflows.

Pre-requisite:

For the course, access to a high-performance computer was organised by trainers

The course will cover:

Logistics:

Venue of course: KEMRI / WELLCOME TRUST Kilifi, Kenya
Start date: 2023-03-27
End date: 2023-03-31

Course curriculum:

Day 1 HPC and introduction to containers
Day 2 Introduction to git and file organisation
Day 3 Introduction to snakemake
Day 4 Advanced workflows (Nextflow, CWL)
Day 5 Practical application

Session	Course materials	Training partner	Interactive Sessions with Instructor/s
9:00am-10:30am	Day 1 slides & files 1. Get started working on HPC 1.1 Confirm participant streams	NGS Academy/UCT	Tony Li Kirsty Lee Garson
10:30am-12:00pm	1.2 Introduction to Conda and Conda environments 1.3 Miniconda Installation 1.4 Use of mamba 1.5 Conda environments 1.6 Different ways of specifying (cmd line, yaml file) 1.7 Ways of saving/exporting/sharing 1.8 Practical 1.9 Lecture	KEMRI	Dr George Githinji
1:00pm-5:00pm	1.9.0 Introduction to Containers 1.9.1 Introduction to docker 1.9.2 Finding and rolling out containers 1.9.3 Run docker 1.9.4 Build a docker container 1.9.5 Modifying a docker container 1.9.6 Sharing a docker container via docker hub 1.9.7 Theory session on singularity, similarities and differences with docker 1.9.8 S materials (CLIMB)	KEMRI	Dr George Githinji

Session	Course materials	Training partner	Interactive Sessions with Instructor/s
9:00am - 10:30am	Day 2 slides & files 2. Introduction to Git 2.1 Software carpentry (Basic Unix and Git)	KEMRI	Dr George Githinji
10:30am - 1:00pm	2.2 Scientific talk	KEMRI	Dr Charles Sande
2:00pm - 5:00pm	2.3 File organisation.	KEMRI	Dr George Githinji

Session	Course materials	Training partner	Interactive Sessions with Instructor/s
9:00am - 1:00pm	Day 3 slides & files 3. Introduction to Snakemake 3.1 Scripting 3.2 Basic concerpts 3.3 Running a basic pipeline 3.4 Configurations 3.5 Combined lecture & practicals (Snakemake)	Malawi-Liverpool-Wellcome Trust	Dr Philip Ashton, Belson Kutambe
2:00pm - 5:00pm	3.6.0 Running snakemake. 3.6.1 Run snakemake with conda 3.6.2 Running snakemake on HPC 3.6.3 Practical: Snakemake	Malawi-Liverpool-Wellcome Trust	Dr Philip Ashton, Belson

Session	Course materials	Training partner	Interactive Sessions with Instructor/s
9:00am - 10:30am	Day 4 slides & files 4.0 Advanced workflows (Nextflow and CWL) 4.1 Compare and contrast with snakemake	ILRI	John Juma
10:30am - 1:00pm	4.2. Nextflow practical	Malawi-Liverpool-Wellcome Trust KEMRI ILRI	Dr Philip Ashton, Belson Kutambe John Juma
2:00pm - 4:00pm	4.3 Practical project work	ILRI KEMRI	John Juma Dr George Githinji

Session	Course materials	Training partner	Interactive Sessions with Instructor/s
9:00am - 1:00pm	Practical project on implementing your own workflow	KEMRI Malawi-Liverpool-Wellcome Trust	Dr George Githinji Dr Philip Ashton John Juma