nf-core pipeline · demo, minimal-example, training
nf-core/demo
A minimal Nextflow pipeline for bioinformatics workshops, demonstrations, and training sessions.
What nf-core/demo is
nf-core/demo is a lightweight bioinformatics pipeline created using the standard nf-core template. Originally developed by Chris Hakkaart and maintained by the Nextflow community team alongside Geraldine Van der Auwera and Florian Wuennemann, it provides a functional yet minimal implementation of an nf-core workflow.
The pipeline addresses the need for a quick-running, accessible example that instructors, trainees, and developers can use during live workshops, tutorials, and practical demonstrations. Rather than handling heavy biological workloads, it executes rapidly using small test datasets to illustrate standard pipeline structures and operational practices.
What the pipeline does
The pipeline takes raw single-end or paired-end sequencing reads in FASTQ format supplied via a comma-separated samplesheet. It begins by performing initial quality control on raw reads using FastQC, followed by adapter and quality trimming executed with seqtk (SEQTK_TRIM).
Once quality trimming and assessment steps complete, the pipeline compiles a unified quality control report across the raw reads using MultiQC. Finally, it executes cowpy to print an ASCII art text message from a cow.
Key facts
- Pipeline engine
- Nextflow
- Original author
- Chris Hakkaart
- Current maintainers
- Nextflow community team, Geraldine Van der Auwera, and Florian Wuennemann
- Latest release
- 1.2.0 (2026-06-24)
- Input format
- CSV samplesheet specifying sample names and single-end or paired-end FASTQ file paths
- Key tools
- FastQC, seqtk, MultiQC, cowpy
What you can use it for
- Bioinformatics training workshops
- Teaching students and researchers how to run and configure Nextflow workflows using quick, small-scale test data.
- Pipeline demonstration
- Demonstrating the standard layout, quality reporting, and behaviour of an nf-core pipeline without long runtimes.
- Nextflow environment verification
- Validating local or cloud Nextflow execution configurations using a minimal workflow before deploying complex pipelines.
Run it here
The research agent runs nf-core/demo with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Executes rapidly because it is designed specifically for small test datasets.
- Follows the standard nf-core template architecture, providing an authentic reference for training.
- Supports both single-end and paired-end FASTQ input configurations.
Watch out for
- Designed purely for training and demonstration rather than comprehensive biological analysis.
- Pipeline parameters cannot be supplied through custom configuration files passed via the -c option.
Questions
Can I run nf-core/demo without my own cluster?
The research agent runs nf-core/demo with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/demo under?
MIT, like every nf-core pipeline.
What inputs does the pipeline accept?
It accepts a CSV samplesheet defining sample names along with paths to single-end FASTQ files or paired-end FASTQ read pairs.
What tools are included in the workflow?
The pipeline runs FastQC for quality control, seqtk for adapter and quality trimming, MultiQC for summary reporting, and cowpy for a text message.
Can pipeline parameters be passed in custom configuration files?
No, pipeline parameters must be provided via the command-line interface or a Nextflow parameters file (-params-file), not through -c configuration files.
How to cite it
10.5281/zenodo.12192442
Written from nf-core/demo's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.