All

191 repositories

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•413•283•217•Updated May 4, 2026May 4, 2026
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
website nextflow nf-core
MDX
•
MIT License
•291•91•116•35•Updated May 4, 2026May 4, 2026
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
nextflow actions
TypeScript
•
MIT License
•5•29•4•8•Updated May 4, 2026May 4, 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•1•Updated May 4, 2026May 4, 2026
strict-syntax-health
Public
Track Nextflow strict syntax linting health across nf-core pipelines
Python
•
MIT License
•4•7•0•0•Updated May 4, 2026May 4, 2026
slackbot
Public
Python
•0•0•0•0•Updated May 2, 2026May 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
•503•160•40•31•Updated May 2, 2026May 2, 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
•239•304•335•36•Updated May 2, 2026May 2, 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
•865•1.3k•24•10•Updated May 1, 2026May 1, 2026
riboseq
Public
Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•18•25•17•6•Updated May 1, 2026May 1, 2026
proteinfamilies
Public
Generation and updating of protein families
workflow bioinformatics pipeline
workflow bioinformatics pipeline nextflow metagenomics protein-families nf-core
Nextflow
•
MIT License
•3•22•7•1•Updated May 1, 2026May 1, 2026
seqsubmit
Public
nf-core pipeline for data submission to ENA
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•5•5•15•5•Updated May 1, 2026May 1, 2026
setup-nf-test
Public
Shell
•
MIT License
•3•7•1•1•Updated May 1, 2026May 1, 2026
stats
Public
evidence
evidence
Python
•3•2•36•8•Updated May 1, 2026May 1, 2026
ops
Public
Different *Ops related scripts for the nf-core org.
Python
•3•3•37•21•Updated May 1, 2026May 1, 2026
pacvar
Public
Longread PacBio sequencing processing for WGS and PureTarget
workflow pipeline nextflow
workflow pipeline nextflow alignment long-read pacbio variant-calling wgs nf-core puretarget
Nextflow
•
MIT License
•10•16•6•4•Updated Apr 30, 2026Apr 30, 2026
cellpainting
Public
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•11•9•8•4•Updated Apr 30, 2026Apr 30, 2026
nf-core-utils
Public
Nextflow plugin for nf-core utils
plugin nextflow nf-core
plugin nextflow nf-core nextflow-plugin nextflow-plugins
Groovy
•
Apache License 2.0
•0•1•11•2•Updated Apr 30, 2026Apr 30, 2026
spatialxe
Public
workflow pipeline nextflow
workflow pipeline nextflow image-processing spatial transcriptomics spatial-data-analysis 10x-genomics nf-core spatial-transcriptomics
Nextflow
•
MIT License
•20•31•32•11•Updated Apr 30, 2026Apr 30, 2026
mspepid
Public
This pipeline performs the peptide identification of MS2 spectra from a proteomics experiment. For this, different search algorithm and rescoring approaches can…
workflow pipeline nextflow
workflow pipeline nextflow proteomics mass-spectrometry nf-core
Nextflow
•
MIT License
•1•3•3•1•Updated Apr 30, 2026Apr 30, 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
•36•79•11•4•Updated Apr 30, 2026Apr 30, 2026
references
Public
nf-core/references is a bioinformatics pipeline that build references, for multiple use cases
workflow pipeline genome
workflow pipeline genome nextflow reproducible-research reproducible-science references reproducibility nf-core
Nextflow
•
MIT License
•6•19•27•2•Updated Apr 30, 2026Apr 30, 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
•528•567•239•41•Updated Apr 30, 2026Apr 30, 2026
pangenome
Public
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
workflow pipeline nextflow
workflow pipeline nextflow pangenome nf-core
Nextflow
•
MIT License
•21•105•11•5•Updated Apr 30, 2026Apr 30, 2026
viralmetagenome
Public
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
workflow pipeline nextflow
workflow pipeline nextflow ngs epidemiology fastq virology viral-metagenomics nf-core virus-genomes
Nextflow
•
MIT License
•9•34•14•2•Updated Apr 30, 2026Apr 30, 2026
hgtseq
Public
A pipeline to investigate horizontal gene transfer from NGS data
taxonomies workflow pipeline
taxonomies workflow pipeline nextflow ngs tidyverse multiqc samtools bwa-mem horizontal-gene-transfer
Nextflow
•
MIT License
•7•26•0•2•Updated Apr 30, 2026Apr 30, 2026
troughgraph
Public
A quantitative assessment of the underlying permafrost landscapes and, per extension, of the level of permafrost thaw in the region
workflow pipeline nextflow
workflow pipeline nextflow permafrost nf-core
Nextflow
•
MIT License
•0•2•0•3•Updated Apr 30, 2026Apr 30, 2026
hadge
Public
Comprehensive pipeline for donor demultiplexing in single cell
workflow pipeline nextflow
workflow pipeline nextflow single-cell deconvolution demultiplexing nf-core donor-deconvolution cell-hashing hto
Nextflow
•
MIT License
•8•25•12•3•Updated Apr 30, 2026Apr 30, 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
•148•161•55•5•Updated Apr 30, 2026Apr 30, 2026
mag
Public
Assembly and binning of metagenomes
workflow bioinformatics nanopore
workflow bioinformatics nanopore pipeline annotation nextflow assembly metagenomics binning metagenomes
Nextflow
•
MIT License
•147•292•72•9•Updated Apr 30, 2026Apr 30, 2026

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nf-core

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191 repositories

modules

website

setup-nextflow

oncoanalyser

strict-syntax-health

slackbot

test-datasets

tools

rnaseq

riboseq

proteinfamilies

seqsubmit

setup-nf-test

stats

ops

pacvar

cellpainting

nf-core-utils

spatialxe

mspepid

hlatyping

references

sarek

pangenome

viralmetagenome

hgtseq

troughgraph

hadge

viralrecon

mag

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191 repositories