nf-core

All

160 repositories

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
•
MIT License
•443•441•275•38•Updated Apr 25, 2025Apr 25, 2025
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•245•75•95•26•Updated Apr 25, 2025Apr 25, 2025
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
•
MIT License
•6•17•5•5•Updated Apr 25, 2025Apr 25, 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
•395•122•33•10•Updated Apr 25, 2025Apr 25, 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
•838•355•485•175•Updated Apr 25, 2025Apr 25, 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
•201•256•272•30•Updated Apr 25, 2025Apr 25, 2025
scrnaseq
Public
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
workflow rna-seq pipeline nextflow single-cell kallisto 10x-genomics 10xgenomics nf-core bustools
Nextflow
•
MIT License
•188•265•61•4•Updated Apr 25, 2025Apr 25, 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
•
MIT License
•112•153•28•1•Updated Apr 25, 2025Apr 25, 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
•305•98•9•17•Updated Apr 25, 2025Apr 25, 2025
demultiplex
Public
Demultiplexing pipeline for sequencing data
nextflow illumina demultiplexing bcl2fastq nf-core bases2fastq elementbiosciences workflow pipeline
Nextflow
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MIT License
•43•46•22•1•Updated Apr 24, 2025Apr 24, 2025
ops
Public
Python
•2•2•30•10•Updated Apr 24, 2025Apr 24, 2025
scdownstream
Public
A single cell transcriptomics pipeline for QC, integration and making the data presentable
workflow quality-control integration pipeline nextflow clustering dimensionality-reduction single-cell nf-core scverse
Nextflow
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MIT License
•23•54•26•1•Updated Apr 24, 2025Apr 24, 2025
methylong
Public
Extract methylation calls from long reads (ONT/ PacBio)
MIT License
•1•5•1•2•Updated Apr 24, 2025Apr 24, 2025
testpipeline
Public
A small example pipeline used to test new nf-core infrastructure and common code.
Nextflow
•
MIT License
•41•5•0•10•Updated Apr 24, 2025Apr 24, 2025
airrflow
Public
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
nextflow nf-core b-cell repseq immcantation immunorepertoire airr workflow pipeline
Nextflow
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MIT License
•41•60•22•5•Updated Apr 24, 2025Apr 24, 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
•
MIT License
•50•144•39•4•Updated Apr 24, 2025Apr 24, 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
•44•99•37•5•Updated Apr 24, 2025Apr 24, 2025
abotyper
Public
A pipeline for characterising the Human Blood Group and Red Cell Antigens using Oxford Nanopore third-generation sequencing data.
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•0•0•0•0•Updated Apr 24, 2025Apr 24, 2025
nascent
Public
Nascent Transcription Processing Pipeline
nextflow rna transcription tss gro-seq nf-core pro-seq nascent workflow pipeline
Nextflow
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MIT License
•11•19•40•5•Updated Apr 24, 2025Apr 24, 2025
proteinannotator
Public
The best protein annotation pipeline in the world. Protein fasta → ??? → Annotations
Nextflow
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MIT License
•3•3•14•5•Updated Apr 23, 2025Apr 23, 2025
genomeqc
Public
Compare the quality of multiple genomes, along with their annotations.
bioinformatics quality-control pipeline genomics nextflow phylogenetic-trees genome-assembly-evaluation nf-core
Nextflow
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MIT License
•16•11•48•5•Updated Apr 23, 2025Apr 23, 2025
methylarray
Public
Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.
Nextflow
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MIT License
•3•4•12•1•Updated Apr 23, 2025Apr 23, 2025
dualrnaseq
Public
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
workflow rna-seq pipeline nextflow quantification nf-core host-pathogen dualrna-seq readmapping
Nextflow
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MIT License
•36•22•37•8•Updated Apr 23, 2025Apr 23, 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
Nextflow
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MIT License
•5•8•2•2•Updated Apr 23, 2025Apr 23, 2025
circrna
Public
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
workflow pipeline genomics nextflow ngs circrna mirna circular-rna circrna-prediction mirna-targets
Nextflow
•
MIT License
•30•54•15•2•Updated Apr 22, 2025Apr 22, 2025
nf-utils
Public
Nextflow plugin for nf-core utils
Groovy
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MIT License
•0•0•0•0•Updated Apr 22, 2025Apr 22, 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
•752•1k•71•14•Updated Apr 22, 2025Apr 22, 2025
genomeassembler
Public
Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
workflow pipeline nextflow genome-assembly nf-core
Nextflow
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MIT License
•15•24•4•1•Updated Apr 22, 2025Apr 22, 2025
references
Public
nf-core/references is a bioinformatics pipeline that build references, for multiple use cases
genome reproducible-research reproducible-science references reproducibility
Nextflow
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MIT License
•5•14•23•2•Updated Apr 22, 2025Apr 22, 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
•18•66•28•5•Updated Apr 22, 2025Apr 22, 2025