nf-core

All

183 repositories

website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•268•85•115•34•Updated Feb 21, 2026Feb 21, 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
•
MIT License
•30•51•15•1•Updated Feb 21, 2026Feb 21, 2026
strict-syntax-health
Public
Track Nextflow strict syntax linting health across nf-core pipelines
Python
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MIT License
•2•7•0•1•Updated Feb 21, 2026Feb 21, 2026
ops
Public
Different *Ops related scripts for the nf-core org.
Python
•3•3•37•24•Updated Feb 20, 2026Feb 20, 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
•58•114•47•3•Updated Feb 20, 2026Feb 20, 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
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MIT License
•847•1.2k•26•15•Updated Feb 20, 2026Feb 20, 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
•967•400•376•162•Updated Feb 20, 2026Feb 20, 2026
hadge
Public
Comprehensive pipeline for donor demultiplexing in single cell
workflow pipeline nextflow single-cell deconvolution demultiplexing nf-core donor-deconvolution cell-hashing hto
Nextflow
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MIT License
•8•25•12•3•Updated Feb 20, 2026Feb 20, 2026
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
•
MIT License
•61•178•45•8•Updated Feb 20, 2026Feb 20, 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
•461•150•36•21•Updated Feb 20, 2026Feb 20, 2026
metapep
Public
From metagenomes to epitopes and beyond
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•8•12•16•2•Updated Feb 20, 2026Feb 20, 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
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MIT License
•10•20•8•1•Updated Feb 20, 2026Feb 20, 2026
seqinspector
Public
Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc rep…
workflow quality-control pipeline genomics nextflow nf-core
Nextflow
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MIT License
•38•19•28•8•Updated Feb 20, 2026Feb 20, 2026
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
•35•101•23•2•Updated Feb 20, 2026Feb 20, 2026
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
•524•549•237•35•Updated Feb 20, 2026Feb 20, 2026
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
•61•98•52•7•Updated Feb 20, 2026Feb 20, 2026
variantprioritization
Public
Analysis pipeline for the functional annotation and translation of somatic SNVs/InDels and copy number abberations for precision cancer medicine.
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•9•12•9•5•Updated Feb 20, 2026Feb 20, 2026
eager
Public
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
workflow bioinformatics pipeline genome nextflow metagenomics population-genetics adna pathogen-genomics nf-core
Nextflow
•
MIT License
•88•199•46•6•Updated Feb 20, 2026Feb 20, 2026
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•4•26•6•2•Updated Feb 20, 2026Feb 20, 2026
variantbenchmarking
Public
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
workflow benchmark pipeline nextflow variant-calling structural-variants nf-core small-variants
Nextflow
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MIT License
•21•40•28•0•Updated Feb 20, 2026Feb 20, 2026
airrflow
Public
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
workflow pipeline nextflow nf-core b-cell repseq immcantation immunorepertoire airr
Nextflow
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MIT License
•47•74•32•4•Updated Feb 19, 2026Feb 19, 2026
proteinannotator
Public
Generation of sequence-level annotations for amino acid sequences
workflow pipeline annotation nextflow proteomics nf-core
Nextflow
•
MIT License
•10•10•22•6•Updated Feb 19, 2026Feb 19, 2026
phaseimpute
Public
A bioinformatics pipeline to phase and impute genetic data
workflow pipeline genomics nextflow imputation genotype phasing low-pass-sequencing
Nextflow
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MIT License
•20•28•19•4•Updated Feb 19, 2026Feb 19, 2026
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 Feb 19, 2026Feb 19, 2026
pharmstarcaller
Public
0•0•0•0•Updated Feb 19, 2026Feb 19, 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
•4•15•1•3•Updated Feb 19, 2026Feb 19, 2026
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•7•Updated Feb 19, 2026Feb 19, 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•2•Updated Feb 19, 2026Feb 19, 2026
tools
Public
Python package with helper tools for the nf-core community.
python workflow bioinformatics pipeline nextflow linting linter nf-core
Python
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MIT License
•224•293•333•42•Updated Feb 19, 2026Feb 19, 2026
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
workflow pipeline nextflow cancer panel ngs clinical dna rna wgs
Nextflow
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MIT License
•27•102•11•6•Updated Feb 18, 2026Feb 18, 2026