nf-core

All

177 repositories

website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
•
MIT License
•254•81•111•20•Updated Dec 11, 2025Dec 11, 2025
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
workflow pipeline nextflow cancer panel ngs clinical dna rna wgs
Nextflow
•
MIT License
•26•97•11•7•Updated Dec 11, 2025Dec 11, 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
•
MIT License
•946•389•389•161•Updated Dec 10, 2025Dec 10, 2025
stats
Public
evidence
HTML
•3•2•38•5•Updated Dec 10, 2025Dec 10, 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
•493•524•307•39•Updated Dec 10, 2025Dec 10, 2025
riboseq
Public
Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•14•18•14•4•Updated Dec 10, 2025Dec 10, 2025
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
•223•283•322•41•Updated Dec 10, 2025Dec 10, 2025
variantprioritization
Public
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•9•10•15•2•Updated Dec 10, 2025Dec 10, 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•4•Updated Dec 10, 2025Dec 10, 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•144•35•15•Updated Dec 10, 2025Dec 10, 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
•827•1.2k•36•15•Updated Dec 10, 2025Dec 10, 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
•5•24•8•3•Updated Dec 10, 2025Dec 10, 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
•
MIT License
•58•85•92•7•Updated Dec 10, 2025Dec 10, 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•17•9•2•Updated Dec 10, 2025Dec 10, 2025
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 reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.
workflow quality-control pipeline genomics nextflow nf-core
Nextflow
•
MIT License
•37•14•33•11•Updated Dec 10, 2025Dec 10, 2025
phaseimpute
Public
A bioinformatics pipeline to phase and impute genetic data
workflow pipeline genomics nextflow imputation genotype phasing low-pass-sequencing
Nextflow
•
MIT License
•20•26•17•9•Updated Dec 10, 2025Dec 10, 2025
nft-utils
Public
nf-test utility functions
nextflow ci-cd nf-test plugin-nf-test
Java
•
MIT License
•10•12•8•2•Updated Dec 10, 2025Dec 10, 2025
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•4•22•5•8•Updated Dec 10, 2025Dec 10, 2025
ops
Public
Different *Ops related scripts for the nf-core org.
Python
•2•3•37•17•Updated Dec 9, 2025Dec 9, 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
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MIT License
•5•26•10•1•Updated Dec 9, 2025Dec 9, 2025
metapep
Public
From metagenomes to epitopes and beyond
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•8•12•15•4•Updated Dec 9, 2025Dec 9, 2025
magmap
Public
Best-practice analysis pipeline for mapping reads to a (large) collections of genomes
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•5•10•6•1•Updated Dec 9, 2025Dec 9, 2025
methylseq
Public
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
workflow pipeline nextflow dna-methylation rrbs methyl-seq epigenomics bisulfite-sequencing nf-core epigenome
Nextflow
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MIT License
•161•182•16•4•Updated Dec 9, 2025Dec 9, 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•9•0•Updated Dec 8, 2025Dec 8, 2025
rnadnavar
Public
Pipeline for RNA and DNA integrated analysis for somatic mutation detection
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•9•12•3•4•Updated Dec 8, 2025Dec 8, 2025
proteinannotator
Public
The best protein annotation pipeline in the world. Protein fasta → ??? → Annotations
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•8•8•21•4•Updated Dec 8, 2025Dec 8, 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
•4•19•2•1•Updated Dec 8, 2025Dec 8, 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•17•1•Updated Dec 8, 2025Dec 8, 2025
rnavar
Public
gatk4 RNA variant calling pipeline
workflow pipeline nextflow rnaseq rna variant-calling nf-core gatk4 worflow
Nextflow
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MIT License
•42•56•18•1•Updated Dec 5, 2025Dec 5, 2025
mag
Public
Assembly and binning of metagenomes
workflow bioinformatics nanopore pipeline annotation nextflow assembly metagenomics binning metagenomes
Nextflow
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MIT License
•142•260•74•9•Updated Dec 5, 2025Dec 5, 2025