All courses Workflow Academy · Course 02 · Intermediate

Developing pipelines on the platform: fundamentals

Build, version and validate your own pipelines on the platform. Wrap your tools in Viash modules and compose them with Nextflow.

Course overview

What you will cover

Five modules over two sessions of four hours each, with hands-on labs throughout.

Module 01

The platform's developer surface

Workspaces, repositories and the Viash Hub
Versioning, releases and the validation lifecycle
How a pipeline gets from your laptop to a scientist's run

Module 02

Wrapping a tool as a Viash module

Module config, typed inputs and outputs
Declaring dependencies and container images
Testing modules locally

Module 03

Composing modules into a Nextflow workflow

Nextflow basics and VDSL3
Wiring modules together with channels
Parameter handling and defaults

Module 04

Publishing and versioning

Auto-build on commit
Releasing a workflow to the catalogue
Maintaining older versions for reproducibility

Module 05

Running your workflow at scale

Compute targets: local, HPC, cloud
Resource configuration and cost considerations
What the scientist sees when they pick up your workflow

Objectives

What you will achieve

Build a Viash module that wraps a real bioinformatics tool.
Compose modules into a working Nextflow workflow on the platform.
Publish a versioned workflow to the catalogue and run it from the UI.

Key take-aways

By the end of the course

You can develop your own pipelines on the platform. Modules are typed and containerised, workflows are versioned, and your team's scientists can run them without touching code.

Required skills

Before you start

Comfortable with the command line. Some scripting experience (Bash, Python or R). Familiar with running existing bioinformatics tools. No prior Nextflow or Viash experience required.

Trainers

Led by

Data Intuitive bioinformatics teamWorking bioinformatics engineers

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