BIO HELP LEARNING COURSE

Reproducible Pipelines with Nextflow, Snakemake, Docker and HPC

Turn analyses into reproducible, scalable pipelines: Git, Conda, Docker and Apptainer containers, Snakemake and Nextflow workflows, nf-core and HPC job scheduling.

Programming

◉ Advanced◷ 20 Hours▣ Certificate Included

Course Information

Everything you need to know before enrolling.

LANGUAGEEnglish

Pre-Register for Live Training

Registration for the next live batch opens soon. Pre-register and our team will contact you with the batch dates, fees and registration link as soon as it opens.

Live online classes
Group & college batches
Certificate on completion

Pre-register for live training → Ask on WhatsApp Or email [email protected]

▤ Overview ☷ Curriculum ♙ Instructor ☆ Reviews ▣ FAQs

▤

About This Course

Modern bioinformatics needs analyses that anyone can rerun on any machine. This course teaches the tools professional teams use to make workflows reproducible, portable and scalable.

You version code with Git, manage software with Conda, package tools in Docker and Apptainer containers, build workflows in Snakemake and Nextflow, run nf-core pipelines, and submit jobs to an HPC cluster with SLURM.

Who this course is for

Bioinformaticians who run the same analyses many times
PhD students and research staff working on clusters
Analysts preparing for industry bioinformatics roles

Prerequisites

Linux and Command Line, plus at least one NGS workflow such as RNA-seq or WGS.

Final project

Wrap an NGS QC-to-alignment workflow in Nextflow or Snakemake with containers, so it reruns from a single command.

◎

What You’ll Learn

✓Version-control analysis code with Git and GitHub

✓Create reproducible software environments with Conda

✓Build and use Docker and Apptainer containers

✓Write Snakemake workflows with rules and wildcards

✓Write Nextflow pipelines with processes and channels

✓Run and configure nf-core pipelines

✓Submit and monitor jobs on HPC with SLURM

⌘

Tools & Technologies

GitGitHubCondaDockerApptainer (Singularity)SnakemakeNextflownf-coreSLURMLinux

Course Curriculum

What you will learn, day by day

10 days 20 hours of training 40 topics Certificate on completion

- Why analyses fail to reproduce
- Git basics: commit, branch, merge
- Working with GitHub
- Project structure for pipelines
- Environment files and version pinning
- Mamba for faster installs
- Sharing environments
- Common dependency problems
- Images and containers
- Writing a Dockerfile
- Running bioinformatics tools in containers
- Using BioContainers
- Why HPC uses Apptainer (Singularity)
- Cluster architecture and storage
- SLURM job scripts
- Monitoring and managing jobs
- Rules, inputs and outputs
- Wildcards and sample tables
- Running Snakemake with Conda and containers
- Visualizing the workflow graph
- Configuration files
- Running on a cluster
- Checkpoints and logging
- Testing a workflow
- Processes and channels
- Writing a first pipeline
- Configuration and profiles
- Resuming failed runs
- Modules and subworkflows
- Running an nf-core pipeline
- Customizing parameters
- Reading pipeline reports
- Running pipelines on HPC and the cloud
- Resource requests and optimization
- Handling hundreds of samples
- Cost and time estimates
- Design a QC-to-alignment pipeline
- Containerize every step
- Test, document and publish to GitHub
- Presentation and code review

♙

Your Instructor

Bio Help Learning Educator

Bioinformatics Educator & Mentor

Learn from experienced educators and practitioners through practical, career-focused bioinformatics training.

Frequently Asked Questions

6 answers about this course

Do I need access to an HPC cluster?

No. You can follow everything on your own computer; HPC sessions show how to transfer it to a cluster when you have access.

Snakemake or Nextflow: which should I learn?

Both are covered. Snakemake feels natural to Python users, and Nextflow powers the nf-core community pipelines.

What should I know before joining?

Comfortable Linux command-line use and at least one NGS workflow.

Will I get a certificate?

Yes, after completing all sessions, the quizzes and the final pipeline project.

How do I get fee and batch details?

Pre-register on this page or contact us on WhatsApp, and our team will share the details.

How long will I have access to the course?

You get full access to all course materials for 3 months from the date of enrollment.

Still have a question?Our team usually replies within one working day.

Ask on WhatsApp →

WHAT OUR LEARNERS SAY

Real Stories. Real Growth.

Hear from learners building practical skills with Bio Help Learning.

★★★★☆

I really enjoyed the course and found it very useful: it gave a clear and practical overview of the whole WGS workflow, from raw reads to a VCF, and the hands-on sessions helped a lot.

Marc Peralta SerranoUniversity of BarcelonaWhole Genome Sequencing (WGS) Data Analysis Training

★★★★★

The workshop provided me an understanding of the principles and techniques involved in bioinformatics, molecular docking, protein-ligand interactions, homology modeling, and drug design.

Ridam BhowmickMaulana Abul Kalam Azad University of Technology, West Bengal.Molecular Docking and Drug Discovery

★★★★★

As i am from biotechnology background this workshop, actually very helpfull for me

Anushka ChavanDeogiri college AurangabadBioinformatics Training

★★★★★

Learn about different molecular docking tools.

Shovan NaskarIndian Institute of Technology (Banaras Hindu University), VaranasiBioinformatics Workshop

★★★★★

This workshop helped me to learn working with various softwares and also to develop an interest over drug designing

Subhodeep SahaUniversity of CalcuttaBioinformatics Training

★★★★★

From this workshop I learned many new things such as docking, about new websites,how to use Swiss software,basic bioinformatics etc, it's very helpful for me.

Sayan DuttaUniversity of CalcuttaBioinformatics Training

★★★★☆

The workshop was informative and provided valuable insights into bioinformatics tools and techniques.

Santhosh M EReva University BangaloreBioinformatics Tools and Techniques

★★★★★

The Drug Discovery Workshop was highly informative and helped me gain valuable knowledge about the drug discovery process, including molecular docking, drug–target interactions, and computational tools used in drug design.

ANUSHA P VCSIR-CCMB, Hyderabad IndiaDrug Discovery Workshop

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OUR GLOBAL LEARNERS