nf-core

All

183 repositories

website
Public
Code and files for the main nf-core website.
website nextflow nf-core
website nextflow nf-core
MDX
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MIT License
•274•85•115•39•Updated Mar 4, 2026Mar 4, 2026
variantbenchmarking
Public
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
workflow benchmark pipeline
workflow benchmark pipeline nextflow variant-calling structural-variants nf-core small-variants
Nextflow
•
MIT License
•21•40•26•1•Updated Mar 4, 2026Mar 4, 2026
epitopeprediction
Public
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
workflow pipeline nextflow
workflow pipeline nextflow epitope-prediction nf-core epitope mhc-binding-prediction
Nextflow
•
MIT License
•31•51•17•3•Updated Mar 4, 2026Mar 4, 2026
raredisease
Public
Call and score variants from WGS/WES of rare disease patients.
workflow pipeline nextflow
workflow pipeline nextflow diagnostics variant-calling wgs snv wes variant-annotation structural-variants
Nextflow
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MIT License
•59•114•47•6•Updated Mar 4, 2026Mar 4, 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
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MIT License
•224•293•333•45•Updated Mar 4, 2026Mar 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
•970•402•423•143•Updated Mar 4, 2026Mar 4, 2026
cageseq
Public
CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
workflow pipeline nextflow
workflow pipeline nextflow gene-expression rna cage nf-core cage-seq cageseq-data
Nextflow
•
MIT License
•12•11•3•7•Updated Mar 4, 2026Mar 4, 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
•61•179•46•9•Updated Mar 4, 2026Mar 4, 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•23•7•0•Updated Mar 4, 2026Mar 4, 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
•56•85•37•4•Updated Mar 4, 2026Mar 4, 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
•59•90•90•9•Updated Mar 4, 2026Mar 4, 2026
hic
Public
Analysis of Chromosome Conformation Capture data (Hi-C)
workflow pipeline nextflow
workflow pipeline nextflow hi-c chromosome-conformation-capture nf-core
Nextflow
•
MIT License
•65•108•43•4•Updated Mar 4, 2026Mar 4, 2026
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
nextflow actions
TypeScript
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MIT License
•4•26•6•6•Updated Mar 4, 2026Mar 4, 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
•34•79•11•2•Updated Mar 4, 2026Mar 4, 2026
mhcquant
Public
Identify and quantify MHC eluted peptides from mass spectrometry raw data
workflow pipeline nextflow
workflow pipeline nextflow dda mhc mass-spectrometry openms peptides nf-core immunopeptidomics
Nextflow
•
MIT License
•33•44•14•2•Updated Mar 4, 2026Mar 4, 2026
pixelator
Public
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
workflow pipeline nextflow
workflow pipeline nextflow proteins pixelator single-cell nf-core single-cell-omics molecular-pixelation pixelgen-technologies
Nextflow
•
MIT License
•9•13•2•0•Updated Mar 4, 2026Mar 4, 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
workflow quality-control pipeline genomics nextflow nf-core
Nextflow
•
MIT License
•38•22•23•8•Updated Mar 4, 2026Mar 4, 2026
proteinfold
Public
Protein 3D structure prediction pipeline
workflow pipeline nextflow
workflow pipeline nextflow protein-structure protein-sequences protein-folding protein-fold-prediction nf-core alphafold2 colabfold
HTML
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MIT License
•61•99•55•7•Updated Mar 4, 2026Mar 4, 2026
ops
Public
Different *Ops related scripts for the nf-core org.
Python
•3•3•37•23•Updated Mar 4, 2026Mar 4, 2026
airrflow
Public
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
workflow pipeline nextflow
workflow pipeline nextflow nf-core b-cell repseq immcantation immunorepertoire airr
Nextflow
•
MIT License
•47•74•33•3•Updated Mar 4, 2026Mar 4, 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 Mar 4, 2026Mar 4, 2026
phaseimpute
Public
A bioinformatics pipeline to phase and impute genetic data
workflow bioinformatics pipeline
workflow bioinformatics pipeline genomics nextflow imputation genotype phasing nf-core low-pass-sequencing
Nextflow
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MIT License
•20•28•19•3•Updated Mar 3, 2026Mar 3, 2026
scnanoseq
Public
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
workflow rna-seq nanopore
workflow rna-seq nanopore pipeline nextflow scrna-seq single-cell 10xgenomics nf-core long-read-sequencing
Nextflow
•
MIT License
•17•51•14•5•Updated Mar 3, 2026Mar 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
•344•107•11•29•Updated Mar 3, 2026Mar 3, 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
•463•151•37•19•Updated Mar 3, 2026Mar 3, 2026
rnavar
Public
gatk4 RNA variant calling pipeline
workflow pipeline nextflow
workflow pipeline nextflow rnaseq rna variant-calling nf-core gatk4 worflow
Nextflow
•
MIT License
•45•59•19•2•Updated Mar 3, 2026Mar 3, 2026
bactmap
Public
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
workflow tree pipeline
workflow tree pipeline genomics nextflow mapping bacteria phylogeny bacterial nf-core
Nextflow
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MIT License
•51•63•4•3•Updated Mar 3, 2026Mar 3, 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
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MIT License
•6•31•10•1•Updated Mar 3, 2026Mar 3, 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
•851•1.2k•32•13•Updated Mar 3, 2026Mar 3, 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
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MIT License
•27•103•11•6•Updated Mar 3, 2026Mar 3, 2026