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nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

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We've verified that the organization nf-core controls the domain:
- nf-co.re
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2.4k followers
http://nf-co.re
@nf-co.re
@[email protected]
company/nf-core
core@nf-co.re

Overview
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Overview
Repositories
Projects
Packages
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Welcome to @nf-core!

@nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow (@nextflow-io).

Here's how to get started:

📚 See available pipelines on the website.
👩‍💻 Check out the documentation.
🙋‍♀️ Come and say hi on our Slack!
🍿 Tune in for talks and events, get involved!
🌈 Please abide by our community code of conduct

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toolstoolsPublic
Python package with helper tools for the nf-core community.
Python 285 223
modulesmodulesPublic
Repository to host tool-specific module files for the Nextflow DSL2 community!
Nextflow 392 951
rnaseqrnaseqPublic
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Nextflow 1.2k 832
sareksarekPublic
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Nextflow 532 499
configsconfigsPublic
Config files used to define parameters specific to compute environments at different Institutions
Nextflow 106 339
proposalsproposalsPublic
Where new ideas for nf-core pipelines, special interest groups and more are proposed
8 3

Repositories

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Showing 10 of 177 repositories

scdownstream Public
A single cell transcriptomics pipeline for QC, integration and making the data presentable
nf-core/scdownstream’s past year of commit activity
Nextflow 81MIT 48 35 (3 issues need help) 2 Updated Jan 10, 2026
website Public
Code and files for the main nf-core website.
nf-core/website’s past year of commit activity
MDX 83MIT 253 114 22 Updated Jan 10, 2026
scrnaseq Public
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
nf-core/scrnaseq’s past year of commit activity
Nextflow 309MIT 206 67 (1 issue needs help) 9 Updated Jan 10, 2026
methylarray Public
Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.
nf-core/methylarray’s past year of commit activity
Nextflow 6MIT 4 8 0 Updated Jan 10, 2026
mag Public
Assembly and binning of metagenomes
nf-core/mag’s past year of commit activity
Nextflow 264MIT 144 74 (1 issue needs help) 11 Updated Jan 10, 2026
setup-nextflow Public
A GitHub action to install Nextflow
nf-core/setup-nextflow’s past year of commit activity
TypeScript 23MIT 4 5 11 Updated Jan 10, 2026
test-datasets Public
Test data to be used for automated testing with the nf-core pipelines
nf-core/test-datasets’s past year of commit activity
150MIT 451 35 17 Updated Jan 9, 2026
ops Public
Different *Ops related scripts for the nf-core org.
nf-core/ops’s past year of commit activity
Python 3 2 37 16 Updated Jan 9, 2026
riboseq Public
Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
nf-core/riboseq’s past year of commit activity
Nextflow 20MIT 17 13 5 Updated Jan 9, 2026
modules Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
nf-core/modules’s past year of commit activity
Nextflow 392MIT 951 389 (1 issue needs help) 164 Updated Jan 9, 2026

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nextflow nf-core pipeline workflow bioinformatics

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