How to Test a nf-core Pipeline | Nextflow Tutorial

Welcome to our channel! In today’s video, we’re diving into the world of testing nf-core pipelines. Whether you’re a bioinformatician, developer, or just curious about how these powerful tools are kept reliable, this video is for you. We’ll explore the key testing strategies used by the nf-core community, from unit tests to continuous integration (CI), ensuring that every pipeline meets the highest standards. Stick around to learn how these testing practices contribute to the robustness and reproducibility of cutting-edge bioinformatics workflows. Let’s get started!”

#nfCore #Bioinformatics #PipelineTesting #ContinuousIntegration #UnitTesting #GitHubActions #Reproducibility #BioinformaticsPipelines #SoftwareDevelopment #OpenScience

nf-core pipelines are set of pipelines based on community effort to collect a curated set of analysis pipelines built using Nextflow.
In this video I will demonstrate how to test nf-core pipelines specifically Sarek and scrnaseq pipelines.

Nextflow lets you run nf-core pipelines on virtually any computing environment. Most nf-core genomics pipelines come with built-in support for AWS-iGenomes, with genome references for over 30 common species.
The nf-core companion tool makes it easy to list all available nf-core pipelines and shows which are available locally. Local versions are checked against the latest available release.

Example of rnaseq:
# Install nextflow
mv nextflow ~/bin/

# Launch the RNAseq pipeline
nextflow run nf-core/rnaseq \
--output ./results/ \
--genome GRCh37 \
-profile docker

# Install nf-core tools
pip install nf-core

# List all nf-core pipelines and show available updates
nf-core list

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