nf-core

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163 repositories

mag
Public
Assembly and binning of metagenomes
workflow nanopore annotation nextflow metagenomics binning nanopore-sequencing nf-core long-read-sequencing bioinformatics
Nextflow
•
MIT License
•132•239•61•8•Updated Jun 21, 2025Jun 21, 2025
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
•
MIT License
•246•76•87•12•Updated Jun 21, 2025Jun 21, 2025
tools
Public
Python package with helper tools for the nf-core community.
bioinformatics linting linter nf-core python workflow pipeline nextflow
Python
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MIT License
•204•260•271•34•Updated Jun 20, 2025Jun 20, 2025
variantbenchmarking
Public
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
workflow benchmark pipeline nextflow draft variant-calling structural-variants nf-core
Nextflow
•
MIT License
•15•29•24•1•Updated Jun 20, 2025Jun 20, 2025
sarek
Public
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
bioinformatics annotation genomics nextflow cancer reproducible-research containers conda next-generation-sequencing variant-calling
Nextflow
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MIT License
•447•451•296•40•Updated Jun 20, 2025Jun 20, 2025
drugresponseeval
Public
Pipeline for testing drug response prediction models in a statistically and biologically sound way.
training workflow machine-learning bioinformatics deep-learning pipeline nextflow reproducible-research cross-validation drugs
Nextflow
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MIT License
•4•20•7•3•Updated Jun 20, 2025Jun 20, 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
•871•356•417•172•Updated Jun 20, 2025Jun 20, 2025
test-datasets
Public
Test data to be used for automated testing with the nf-core pipelines
testing workflow nextflow test-data nf-core pipelines test-datasets
MIT License
•414•130•34•15•Updated Jun 20, 2025Jun 20, 2025
deepmodeloptim
Public
Stochastic Testing and Input Manipulation for Unbiased Learning Systems
workflow pipeline genomics nextflow optimization artificial-intelligence deeplearning large-scale dataprocessing nf-core
Nextflow
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MIT License
•14•29•18•2•Updated Jun 20, 2025Jun 20, 2025
eager
Public
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
workflow metagenomics population-genetics adna pathogen-genomics nf-core ancientdna bioinformatics pipeline genome
Nextflow
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MIT License
•83•171•45•7•Updated Jun 20, 2025Jun 20, 2025
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
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MIT License
•50•79•70•7•Updated Jun 20, 2025Jun 20, 2025
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
•20•75•23•3•Updated Jun 20, 2025Jun 20, 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•4•7•0•Updated Jun 20, 2025Jun 20, 2025
magmap
Public
Best-practice analysis pipeline for mapping reads to a (large) collections of genomes
Nextflow
•
MIT License
•4•6•7•1•Updated Jun 19, 2025Jun 19, 2025
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
•311•99•8•10•Updated Jun 19, 2025Jun 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
•111•159•30•4•Updated Jun 19, 2025Jun 19, 2025
phaseimpute
Public
A bioinformatics pipeline to phase and impute genetic data
pipeline genomics imputation genotype phasing low-pass-sequencing
Nextflow
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MIT License
•20•22•12•0•Updated Jun 19, 2025Jun 19, 2025
ops
Public
Python
•2•2•33•11•Updated Jun 19, 2025Jun 19, 2025
crisprseq
Public
A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
workflow pipeline nextflow ngs crispr-analysis crispr nf-core crispr-cas
Nextflow
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MIT License
•31•46•26•2•Updated Jun 19, 2025Jun 19, 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
•53•154•38•6•Updated Jun 19, 2025Jun 19, 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
•8•12•6•0•Updated Jun 19, 2025Jun 19, 2025
tfactivity
Public
Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
workflow transcription-factors pipeline nextflow transcriptomics nf-core open-chromatin-regions
Nextflow
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MIT License
•5•12•2•0•Updated Jun 19, 2025Jun 19, 2025
metatdenovo
Public
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
workflow pipeline nextflow metagenomics viruses metatranscriptomics prokaryotes eukaryotes nf-core
Nextflow
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MIT License
•16•33•10•0•Updated Jun 19, 2025Jun 19, 2025
drop
Public
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•2•4•2•6•Updated Jun 18, 2025Jun 18, 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
•1•5•30•4•Updated Jun 18, 2025Jun 18, 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
•26•87•18•2•Updated Jun 18, 2025Jun 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
•29•36•8•5•Updated Jun 18, 2025Jun 18, 2025
createpanelrefs
Public
Generate Panel of Normals, models or other similar references from lots of samples
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•10•9•6•2•Updated Jun 18, 2025Jun 18, 2025
pixelator
Public
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
nextflow proteins pixelator single-cell nf-core single-cell-omics molecular-pixelation pixelgen-technologies workflow pipeline
Nextflow
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MIT License
•6•10•1•3•Updated Jun 18, 2025Jun 18, 2025
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 pipeline nextflow image-processing spatial transcriptomics single-cell microscopy
Nextflow
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MIT License
•25•64•5•2•Updated Jun 18, 2025Jun 18, 2025