nf-core

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185 repositories

proteinannotator
Public
Generation of sequence-level annotations for amino acid sequences
workflow pipeline annotation
workflow pipeline annotation nextflow proteomics nf-core
Nextflow
•
MIT License
•10•11•23•8•Updated Mar 14, 2026Mar 14, 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
•1k•404•362•189•Updated Mar 14, 2026Mar 14, 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
•27•41•33•3•Updated Mar 14, 2026Mar 14, 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
•
MIT License
•64•99•78•17•Updated Mar 14, 2026Mar 14, 2026
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
website nextflow nf-core
MDX
•
MIT License
•285•86•132•36•Updated Mar 14, 2026Mar 14, 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
•479•153•39•23•Updated Mar 14, 2026Mar 14, 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
•231•295•331•49•Updated Mar 14, 2026Mar 14, 2026
ops
Public
Different *Ops related scripts for the nf-core org.
Python
•3•3•37•23•Updated Mar 14, 2026Mar 14, 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
•348•108•12•31•Updated Mar 14, 2026Mar 14, 2026
strict-syntax-health
Public
Track Nextflow strict syntax linting health across nf-core pipelines
Python
•
MIT License
•3•7•0•1•Updated Mar 14, 2026Mar 14, 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
•
MIT License
•60•114•47•7•Updated Mar 13, 2026Mar 13, 2026
slackbot
Public
Python
•0•0•0•0•Updated Mar 13, 2026Mar 13, 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
•20•52•16•3•Updated Mar 13, 2026Mar 13, 2026
longraredisease
Public
Long read sequencing pipeline to identify variants in patients with neurodevelopmental disorders
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•3•7•0•1•Updated Mar 13, 2026Mar 13, 2026
genephylomodeler
Public
A bioinformatics pipeline that fits evolutionary models and performs hypothesis testing on multiple sequence alignments
workflow pipeline nextflow
workflow pipeline nextflow phylogenetics msa nf-core evolutionary-models
Nextflow
•
MIT License
•0•0•4•1•Updated Mar 13, 2026Mar 13, 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
•50•75•33•3•Updated Mar 13, 2026Mar 13, 2026
stats
Public
evidence
evidence
Python
•3•2•36•4•Updated Mar 13, 2026Mar 13, 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
•39•24•26•5•Updated Mar 13, 2026Mar 13, 2026
variantprioritization
Public
Analysis pipeline for the functional annotation and translation of somatic SNVs/InDels and copy number aberations for precision cancer medicine.
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•9•12•3•4•Updated Mar 13, 2026Mar 13, 2026
proteinfamilies
Public
Generation and updating of protein families
workflow bioinformatics pipeline
workflow bioinformatics pipeline nextflow metagenomics protein-families nf-core
Nextflow
•
MIT License
•2•23•7•0•Updated Mar 13, 2026Mar 13, 2026
ribomsqc
Public
QC pipeline that monitors mass spectrometer performance in ribonucleoside analysis
workflow pipeline nextflow
workflow pipeline nextflow nf-core
R
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MIT License
•2•0•0•0•Updated Mar 13, 2026Mar 13, 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
•7•31•8•1•Updated Mar 13, 2026Mar 13, 2026
magmap
Public
Best-practice analysis pipeline for mapping reads to a (large) collections of genomes
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•6•10•10•0•Updated Mar 13, 2026Mar 13, 2026
seqsubmit
Public
nf-core pipeline for data submission to ENA
workflow pipeline nextflow
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•4•3•10•4•Updated Mar 13, 2026Mar 13, 2026
lsmquant
Public
A pipeline for processing and analysis of light-sheet microscopy images.
pipeline nextflow image-processing
pipeline nextflow image-processing stitching segmentation image-analysis nf-core light-sheet-microcopy 3dunet
Nextflow
•
MIT License
•3•5•1•2•Updated Mar 13, 2026Mar 13, 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 13, 2026Mar 13, 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•19•4•Updated Mar 13, 2026Mar 13, 2026
spatialvi
Public
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
workflow bioinformatics rna-seq
workflow bioinformatics rna-seq pipeline nextflow image-processing spatial transcriptomics single-cell microscopy
Nextflow
•
MIT License
•33•72•2•0•Updated Mar 13, 2026Mar 13, 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•14•2•Updated Mar 13, 2026Mar 13, 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
•147•159•55•6•Updated Mar 13, 2026Mar 13, 2026