nf-core pipeline · nanostring, nanostringnorm
nf-core/nanostring
A bioinformatics pipeline for quality control and normalisation of NanoString nCounter gene expression data.
What nf-core/nanostring is
nf-core/nanostring is a bioinformatics pipeline engineered to process expression data from the NanoString nCounter platform. Originally created by Alexander Peltzer and Christopher Mohr, with scientific and technical input from Kai Stadermann, Matthias Zwick, Germán Leparc, and Ramona Schmid, it provides a standardised framework for handling multiplexed hybridization assays.
The pipeline resolves the need for automated quality assessment and data standardisation in NanoString experiments. By processing raw counts into normalised expression tables and compiling aggregated quality summaries, it provides research-ready outputs for downstream statistical analyses.
What the pipeline does
The workflow accepts a comma-separated samplesheet pointing to raw NanoString Reporter Code Count (RCC) files. It applies NACHO to perform quality control assessments and execute normalisation across the dataset.
Following normalisation, the pipeline builds count tables integrated with provided sample metadata. Overall quality control statistics and metrics from the run are then assembled and visualised using MultiQC.
Key facts
- Workflow manager
- Nextflow (DSL2)
- Input format
- RCC files via CSV samplesheet
- Primary tools
- NACHO, MultiQC
- Supported containers
- Docker, Singularity
- Original authors
- Alexander Peltzer, Christopher Mohr
- Latest release
- 1.3.3 (2026-01-30)
What you can use it for
- Quality control of nCounter data
- Inspect assay metrics, technical controls, and sample quality across NanoString runs using NACHO and MultiQC.
- NanoString count normalisation
- Normalise raw RCC counts using NACHO to remove technical variation across samples.
- Expression count table generation
- Combine normalised count matrices with user-defined sample metadata for downstream transcriptomic analysis.
Run it here
The research agent runs nf-core/nanostring 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
- Uses Docker and Singularity containers on a per-process basis to ensure reproducible execution across different compute platforms.
- Leverages community-reviewed nf-core modules for pipeline processes.
- Generates unified MultiQC reports to evaluate data quality in a single view.
Watch out for
- Only accepts raw NanoString data in RCC file format.
- Pipeline parameters cannot be supplied through custom configuration files using the Nextflow -c option; they must be provided via the command line or a parameters file.
Questions
Can I run nf-core/nanostring without my own cluster?
The research agent runs nf-core/nanostring 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/nanostring under?
MIT, like every nf-core pipeline.
What inputs are needed to run nf-core/nanostring?
The pipeline requires a CSV samplesheet with columns designated for the RCC file path, RCC file name, and sample identifier.
Which software performs the normalisation step?
Normalisation and associated quality control steps are executed using NACHO.
How are the quality control outputs presented?
Quality control summaries are consolidated and displayed using MultiQC.
Can pipeline parameters be passed through standard -c configuration files?
No, parameters must be provided via the command-line interface or using a Nextflow -params-file option, as custom configuration files cannot define pipeline parameters.
How to cite it
doi: 10.1093/bioinformatics/btae019/7517109
Written from nf-core/nanostring's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.