nf-core

All

177 repositories

website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•253•83•114•20•Updated Jan 8, 2026Jan 8, 2026
differentialabundance
Public
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
workflow rna-seq pipeline nextflow shiny deseq2 microarray chip-seq atac-seq differential-expression
Nextflow
•
MIT License
•58•87•96•9•Updated Jan 7, 2026Jan 7, 2026
longraredisease
Public
Long read sequencing pipeline to identify variants in patients with neurodevelopmental disorders
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•2•5•1•0•Updated Jan 7, 2026Jan 7, 2026
test-datasets
Public
Test data to be used for automated testing with the nf-core pipelines
testing workflow nextflow pipelines test-data test-datasets nf-core
MIT License
•450•150•35•18•Updated Jan 7, 2026Jan 7, 2026
mhcquant
Public
Identify and quantify MHC eluted peptides from mass spectrometry raw data
workflow pipeline nextflow dda mhc mass-spectrometry openms peptides nf-core immunopeptidomics
Nextflow
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MIT License
•30•42•12•2•Updated Jan 7, 2026Jan 7, 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 nextflow rna nf-core
Nextflow
•
MIT License
•830•1.2k•35•11•Updated Jan 7, 2026Jan 7, 2026
modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
modules nextflow pipelines workflows nf-core dsl2 nf-test
Nextflow
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MIT License
•950•392•388•165•Updated Jan 7, 2026Jan 7, 2026
smrnaseq
Public
A small-RNA sequencing analysis pipeline
workflow pipeline nextflow small-rna nf-core smrna-seq
Nextflow
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MIT License
•131•98•10•0•Updated Jan 7, 2026Jan 7, 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
workflow rna-seq pipeline nextflow single-cell kallisto 10x-genomics 10xgenomics nf-core bustools
Nextflow
•
MIT License
•206•309•73•8•Updated Jan 7, 2026Jan 7, 2026
mag
Public
Assembly and binning of metagenomes
workflow bioinformatics nanopore pipeline annotation nextflow assembly metagenomics binning metagenomes
Nextflow
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MIT License
•144•264•74•10•Updated Jan 7, 2026Jan 7, 2026
raredisease
Public
Call and score variants from WGS/WES of rare disease patients.
workflow pipeline nextflow diagnostics variant-calling wgs snv wes variant-annotation structural-variants
Nextflow
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MIT License
•55•112•48•4•Updated Jan 7, 2026Jan 7, 2026
nanostring
Public
An analysis pipeline for Nanostring nCounter expression data.
workflow pipeline nextflow nanostring nanostringnorm nf-core
Nextflow
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MIT License
•12•16•5•1•Updated Jan 7, 2026Jan 7, 2026
sopa
Public
Nextflow version of Sopa - spatial omics pipeline and analysis
workflow pipeline nextflow segmentation spatial-proteomics nf-core spatial-transcriptomics spatialdata spatial-omics
Nextflow
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MIT License
•1•11•2•3•Updated Jan 7, 2026Jan 7, 2026
viralmetagenome
Public
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
workflow pipeline nextflow ngs epidemiology fastq virology viral-metagenomics nf-core virus-genomes
Nextflow
•
MIT License
•5•27•10•1•Updated Jan 6, 2026Jan 6, 2026
configs
Public
Config files used to define parameters specific to compute environments at different Institutions
bioinformatics nextflow configuration pipelines workflows nf-core
Nextflow
•
MIT License
•339•106•10•17•Updated Jan 6, 2026Jan 6, 2026
createtaxdb
Public
Parallelised and automated construction of metagenomic classifier databases of different tools
workflow database pipeline nextflow metagenomics profiling nf-core database-builder taxonomic-profiling metagenomic-profiling
Nextflow
•
MIT License
•10•20•8•1•Updated Jan 6, 2026Jan 6, 2026
nf-core-utils
Public
Nextflow plugin for nf-core utils
plugin nextflow nf-core nextflow-plugin nextflow-plugins
Groovy
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Apache License 2.0
•0•1•10•2•Updated Jan 5, 2026Jan 5, 2026
riboseq
Public
Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•17•20•13•5•Updated Jan 5, 2026Jan 5, 2026
scdownstream
Public
A single cell transcriptomics pipeline for QC, integration and making the data presentable
workflow quality-control integration pipeline nextflow clustering dimensionality-reduction single-cell nf-core scverse
Nextflow
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MIT License
•47•81•35•7•Updated Jan 2, 2026Jan 2, 2026
lsmquant
Public
A pipeline for processing and analysis of light-sheet microscopy images.
pipeline nextflow image-processing stitching segmentation image-analysis nf-core light-sheet-microcopy 3dunet
Nextflow
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MIT License
•1•5•0•5•Updated Jan 2, 2026Jan 2, 2026
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•4•23•5•11•Updated Jan 2, 2026Jan 2, 2026
epitopeprediction
Public
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
workflow pipeline nextflow epitope-prediction nf-core epitope mhc-binding-prediction
Nextflow
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MIT License
•29•49•14•4•Updated Dec 31, 2025Dec 31, 2025
sarek
Public
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
workflow bioinformatics pipeline annotation genomics nextflow cancer reproducible-research containers conda
Nextflow
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MIT License
•500•529•313•38•Updated Dec 30, 2025Dec 30, 2025
cageseq
Public
CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
workflow pipeline nextflow gene-expression rna cage nf-core cage-seq cageseq-data
Nextflow
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MIT License
•12•11•3•6•Updated Dec 24, 2025Dec 24, 2025
demultiplex
Public
Demultiplexing pipeline for sequencing data
workflow pipeline nextflow illumina demultiplexing bcl2fastq nf-core bases2fastq elementbiosciences
Nextflow
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MIT License
•46•52•24•0•Updated Dec 23, 2025Dec 23, 2025
funcscan
Public
(Meta-)genome screening for functional and natural product gene sequences
workflow bioinformatics pipeline nextflow amp assembly function metagenomics amr screening
Nextflow
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MIT License
•33•99•23•1•Updated Dec 21, 2025Dec 21, 2025
diseasemodulediscovery
Public
A pipeline for network-based disease module identification.
pipeline nextflow systems-biology drug-repurposing networks protein-protein-interaction nf-core protein-protein-interaction-network disease-modules disease-mechanisms
Python
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MIT License
•3•5•35•5•Updated Dec 19, 2025Dec 19, 2025
proteinfold
Public
Protein 3D structure prediction pipeline
workflow pipeline nextflow protein-structure protein-sequences protein-folding protein-fold-prediction nf-core alphafold2 colabfold
HTML
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MIT License
•60•94•55•4•Updated Dec 19, 2025Dec 19, 2025
methylong
Public
Extract methylation calls from long reads (ONT/ PacBio)
workflow pipeline nextflow long-read pacbio dna-methylation ont nf-core fiber-seq
Nextflow
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MIT License
•6•19•2•1•Updated Dec 19, 2025Dec 19, 2025
rnafusion
Public
RNA-seq analysis pipeline for detection of gene-fusions
workflow rna-seq pipeline nextflow gene-fusion fusion rna fusion-genes nf-core
Nextflow
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MIT License
•120•170•18•5•Updated Dec 19, 2025Dec 19, 2025