nf-core

All

177 repositories

setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•4•22•5•8•Updated Dec 13, 2025Dec 13, 2025
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•254•81•111•22•Updated Dec 13, 2025Dec 13, 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
•946•389•389•160•Updated Dec 13, 2025Dec 13, 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•323•42•Updated Dec 13, 2025Dec 13, 2025
riboseq
Public
Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•14•18•14•3•Updated Dec 12, 2025Dec 12, 2025
ops
Public
Different *Ops related scripts for the nf-core org.
Python
•2•3•37•17•Updated Dec 12, 2025Dec 12, 2025
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
•1•11•1•2•Updated Dec 12, 2025Dec 12, 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
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MIT License
•37•14•30•8•Updated Dec 12, 2025Dec 12, 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
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MIT License
•494•527•307•39•Updated Dec 12, 2025Dec 12, 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
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MIT License
•55•112•47•5•Updated Dec 12, 2025Dec 12, 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•0•Updated Dec 12, 2025Dec 12, 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 12, 2025Dec 12, 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•9•0•Updated Dec 12, 2025Dec 12, 2025
configs
Public
Config files used to define parameters specific to compute environments at different Institutions
bioinformatics nextflow configuration pipelines workflows nf-core
Nextflow
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MIT License
•339•104•10•17•Updated Dec 12, 2025Dec 12, 2025
metapep
Public
From metagenomes to epitopes and beyond
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•8•12•16•3•Updated Dec 12, 2025Dec 12, 2025
pacvar
Public
Longread PacBio sequencing processing for WGS and PureTarget
workflow pipeline nextflow alignment long-read pacbio variant-calling wgs nf-core puretarget
Nextflow
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MIT License
•9•12•6•5•Updated Dec 12, 2025Dec 12, 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 12, 2025Dec 12, 2025
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•26•16•8•Updated Dec 12, 2025Dec 12, 2025
nft-utils
Public
nf-test utility functions
nextflow ci-cd nf-test plugin-nf-test
Java
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MIT License
•10•12•8•1•Updated Dec 12, 2025Dec 12, 2025
pixelator
Public
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
workflow pipeline nextflow proteins pixelator single-cell nf-core single-cell-omics molecular-pixelation pixelgen-technologies
Nextflow
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MIT License
•8•13•2•1•Updated Dec 12, 2025Dec 12, 2025
methylseq
Public
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
workflow pipeline nextflow dna-methylation rrbs methyl-seq epigenomics bisulfite-sequencing taps nf-core
Nextflow
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MIT License
•161•182•16•3•Updated Dec 12, 2025Dec 12, 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
•450•145•35•15•Updated Dec 12, 2025Dec 12, 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
•828•1.2k•33•11•Updated Dec 12, 2025Dec 12, 2025
ampliseq
Public
Amplicon sequencing analysis workflow using DADA2 and QIIME2
workflow pipeline nextflow metagenomics pacbio edna microbiome iontorrent illumina metabarcoding
Nextflow
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MIT License
•146•227•20•2•Updated Dec 12, 2025Dec 12, 2025
meerpipe
Public
nf-core/meerpipe is a astronomy pipeline that processes MeerKAT pulsar data to produce images and data products for pulsar timing analysis
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•5•10•6•1•Updated Dec 12, 2025Dec 12, 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
•27•97•10•6•Updated Dec 11, 2025Dec 11, 2025
demultiplex
Public
Demultiplexing pipeline for sequencing data
workflow pipeline nextflow illumina demultiplexing bcl2fastq nf-core bases2fastq elementbiosciences
Nextflow
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MIT License
•46•51•24•0•Updated Dec 11, 2025Dec 11, 2025
tumourevo
Public
Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
workflow quality-control pipeline nextflow cancer-genomics population-genetics copy-number-variation variant-annotation mutational-signatures cancer-evolution
Nextflow
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MIT License
•5•20•4•2•Updated Dec 11, 2025Dec 11, 2025
hlatyping
Public
Precision HLA typing from next-generation sequencing data
workflow pipeline nextflow dna rna immunology hla optitype hla-typing personalized-medicine
Nextflow
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MIT License
•33•75•11•4•Updated Dec 11, 2025Dec 11, 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
•58•86•92•6•Updated Dec 11, 2025Dec 11, 2025