All

188 repositories

website
Public
Code and files for the main nf-core website.
website nextflow nf-core
website nextflow nf-core
MDX
•
MIT License
•284•88•116•31•Updated Apr 4, 2026Apr 4, 2026
modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
modules nextflow pipelines
modules nextflow pipelines workflows nf-core dsl2 nf-test
Nextflow
•
MIT License
•1k•408•334•196•Updated Apr 4, 2026Apr 4, 2026
ops
Public
Different *Ops related scripts for the nf-core org.
Python
•3•3•37•24•Updated Apr 4, 2026Apr 4, 2026
strict-syntax-health
Public
Track Nextflow strict syntax linting health across nf-core pipelines
Python
•
MIT License
•4•7•0•0•Updated Apr 4, 2026Apr 4, 2026
rnaseq
Public
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
workflow rna-seq pipeline
workflow rna-seq pipeline nextflow rna nf-core
Nextflow
•
MIT License
•857•1.2k•31•17•Updated Apr 3, 2026Apr 3, 2026
taxprofiler
Public
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
workflow bioinformatics nanopore
workflow bioinformatics nanopore pipeline nextflow shotgun pathogen metagenomics classification profiling
Nextflow
•
MIT License
•64•184•41•6•Updated Apr 3, 2026Apr 3, 2026
configs
Public
Config files used to define parameters specific to compute environments at different Institutions
bioinformatics nextflow configuration
bioinformatics nextflow configuration pipelines workflows nf-core
Nextflow
•
MIT License
•351•108•12•27•Updated Apr 3, 2026Apr 3, 2026
tools
Public
Python package with helper tools for the nf-core community.
python workflow bioinformatics
python workflow bioinformatics pipeline nextflow linting linter nf-core
Python
•
MIT License
•236•297•328•57•Updated Apr 3, 2026Apr 3, 2026
spatialvi
Public
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
workflow bioinformatics rna-seq
workflow bioinformatics rna-seq pipeline nextflow image-processing spatial transcriptomics single-cell microscopy
Nextflow
•
MIT License
•32•72•2•1•Updated Apr 3, 2026Apr 3, 2026
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
nextflow actions
TypeScript
•
MIT License
•4•28•6•9•Updated Apr 3, 2026Apr 3, 2026
tandemrepeat
Public
Nextflow
•0•0•0•0•Updated Apr 3, 2026Apr 3, 2026
magmap
Public
Best-practice analysis pipeline for mapping reads to a (large) collections of genomes
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•6•10•6•1•Updated Apr 3, 2026Apr 3, 2026
fastquorum
Public
Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
workflow pipeline nextflow
workflow pipeline nextflow consensus umi unique-molecular-identifier nf-core umis
Nextflow
•
MIT License
•15•27•12•1•Updated Apr 2, 2026Apr 2, 2026
test-datasets
Public
Test data to be used for automated testing with the nf-core pipelines
testing workflow nextflow
testing workflow nextflow pipelines test-data test-datasets nf-core
MIT License
•487•157•38•25•Updated Apr 2, 2026Apr 2, 2026
funcprofiler
Public
Read-based functional profiling of microbiome sequencing data
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•3•2•12•2•Updated Apr 2, 2026Apr 2, 2026
methylseq
Public
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
workflow pipeline nextflow
workflow pipeline nextflow dna-methylation rrbs methyl-seq epigenomics bisulfite-sequencing taps nf-core
Nextflow
•
MIT License
•171•189•21•7•Updated Apr 2, 2026Apr 2, 2026
scdownstream
Public
A single cell transcriptomics pipeline for QC, integration and making the data presentable
workflow quality-control integration
workflow quality-control integration pipeline nextflow clustering dimensionality-reduction single-cell nf-core scverse
Nextflow
•
MIT License
•61•91•38•6•Updated Apr 2, 2026Apr 2, 2026
tumourevo
Public
Analysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature de…
workflow quality-control pipeline
workflow quality-control pipeline nextflow cancer-genomics population-genetics copy-number-variation variant-annotation mutational-signatures cancer-evolution
Nextflow
•
MIT License
•5•20•3•2•Updated Apr 2, 2026Apr 2, 2026
differentialabundance
Public
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
workflow rna-seq pipeline
workflow rna-seq pipeline nextflow shiny deseq2 microarray chip-seq atac-seq differential-expression
Nextflow
•
MIT License
•61•91•89•6•Updated Apr 2, 2026Apr 2, 2026
hlatyping
Public
Precision HLA typing from next-generation sequencing data
workflow pipeline nextflow
workflow pipeline nextflow dna rna immunology hla optitype hla-typing personalized-medicine
Nextflow
•
MIT License
•37•79•11•2•Updated Apr 2, 2026Apr 2, 2026
methylong
Public
Extract methylation calls from long reads (ONT/ PacBio)
workflow pipeline nextflow
workflow pipeline nextflow long-read pacbio dna-methylation ont nf-core fiber-seq
Nextflow
•
MIT License
•6•23•2•1•Updated Apr 2, 2026Apr 2, 2026
sarek
Public
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
workflow bioinformatics pipeline
workflow bioinformatics pipeline annotation genomics nextflow cancer reproducible-research containers conda
Nextflow
•
MIT License
•525•555•236•35•Updated Apr 2, 2026Apr 2, 2026
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
workflow pipeline nextflow
workflow pipeline nextflow cancer panel ngs clinical dna rna wgs
Nextflow
•
MIT License
•28•106•14•6•Updated Apr 2, 2026Apr 2, 2026
drop
Public
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•6•8•4•1•Updated Apr 2, 2026Apr 2, 2026
mag
Public
Assembly and binning of metagenomes
workflow bioinformatics nanopore
workflow bioinformatics nanopore pipeline annotation nextflow assembly metagenomics binning metagenomes
Nextflow
•
MIT License
•148•284•79•9•Updated Apr 2, 2026Apr 2, 2026
abotyper
Public
A pipeline for characterising the Human Blood Group and Red Cell Antigens using Oxford Nanopore third-generation sequencing data.
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•1•3•0•1•Updated Apr 2, 2026Apr 2, 2026
msproteomics
Public
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•0•0•0•0•Updated Apr 2, 2026Apr 2, 2026
cellpainting
Public
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•6•8•14•6•Updated Apr 2, 2026Apr 2, 2026
viralrecon
Public
Assembly and intrahost/low-frequency variant calling for viral samples
workflow nanopore virus
workflow nanopore virus pipeline nextflow assembly metagenomics variant-calling illumina oxford-nanopore
Nextflow
•
MIT License
•147•160•55•4•Updated Apr 1, 2026Apr 1, 2026
stats
Public
evidence
evidence
Python
•3•2•36•5•Updated Apr 1, 2026Apr 1, 2026

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nf-core

All

All

188 repositories

website

modules

ops

strict-syntax-health

rnaseq

taxprofiler

configs

tools

spatialvi

setup-nextflow

tandemrepeat

magmap

fastquorum

test-datasets

funcprofiler

methylseq

scdownstream

tumourevo

differentialabundance

hlatyping

methylong

sarek

oncoanalyser

drop

mag

abotyper

msproteomics

cellpainting

viralrecon

stats

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Repositories list

188 repositories