nf-core

All

177 repositories

website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
•
MIT License
•253•83•112•20•Updated Dec 31, 2025Dec 31, 2025
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
•951•392•392•164•Updated Dec 30, 2025Dec 30, 2025
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•11•Updated Dec 30, 2025Dec 30, 2025
nanostring
Public
An analysis pipeline for Nanostring nCounter expression data.
workflow pipeline nextflow nanostring nanostringnorm nf-core
Nextflow
•
MIT License
•11•16•7•3•Updated Dec 30, 2025Dec 30, 2025
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•4•23•5•11•Updated Dec 30, 2025Dec 30, 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
•
MIT License
•499•528•312•38•Updated Dec 30, 2025Dec 30, 2025
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
•
MIT License
•1•5•0•4•Updated Dec 29, 2025Dec 29, 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
•
MIT License
•12•11•3•6•Updated Dec 24, 2025Dec 24, 2025
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
•28•49•14•4•Updated Dec 24, 2025Dec 24, 2025
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•12•1•Updated Dec 23, 2025Dec 23, 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•23•0•Updated Dec 23, 2025Dec 23, 2025
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•9•0•Updated Dec 22, 2025Dec 22, 2025
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
•
MIT License
•55•112•47•5•Updated Dec 22, 2025Dec 22, 2025
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
•449•147•35•15•Updated Dec 22, 2025Dec 22, 2025
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
•
MIT License
•1•11•1•3•Updated Dec 22, 2025Dec 22, 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
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•6•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•92•54•4•Updated Dec 19, 2025Dec 19, 2025
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
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MIT License
•829•1.2k•35•12•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•169•18•5•Updated Dec 19, 2025Dec 19, 2025
proteinfamilies
Public
Generation and updating of protein families
workflow bioinformatics pipeline nextflow metagenomics proteomics protein-families nf-core
Nextflow
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MIT License
•3•21•7•0•Updated Dec 19, 2025Dec 19, 2025
sammyseq
Public
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
workflow bioinformatics pipeline genomics genome nextflow ngs sequencing next-generation-sequencing dna
Nextflow
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MIT License
•15•5•5•1•Updated Dec 19, 2025Dec 19, 2025
ampliseq
Public
Amplicon sequencing analysis workflow using DADA2 and QIIME2
workflow pipeline nextflow metagenomics pacbio edna microbiome iontorrent illumina metabarcoding
Nextflow
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MIT License
•147•230•21•2•Updated Dec 19, 2025Dec 19, 2025
ops
Public
Different *Ops related scripts for the nf-core org.
Python
•2•3•37•16•Updated Dec 18, 2025Dec 18, 2025
methylseq
Public
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
workflow pipeline nextflow dna-methylation rrbs methyl-seq epigenomics bisulfite-sequencing taps nf-core
Nextflow
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MIT License
•163•184•14•4•Updated Dec 18, 2025Dec 18, 2025
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
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MIT License
•10•20•8•0•Updated Dec 18, 2025Dec 18, 2025
taxprofiler
Public
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
workflow bioinformatics nanopore pipeline nextflow shotgun pathogen metagenomics classification profiling
Nextflow
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MIT License
•59•175•45•7•Updated Dec 18, 2025Dec 18, 2025
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•3•Updated Dec 18, 2025Dec 18, 2025