nf-core

All

158 repositories

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
•837•352•507•182•Updated Apr 16, 2025Apr 16, 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
•7•9•10•1•Updated Apr 16, 2025Apr 16, 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
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MIT License
•13•28•20•0•Updated Apr 16, 2025Apr 16, 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•271•35•Updated Apr 16, 2025Apr 16, 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
•45•78•62•5•Updated Apr 16, 2025Apr 16, 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
•440•440•281•38•Updated Apr 16, 2025Apr 16, 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
•110•153•37•7•Updated Apr 16, 2025Apr 16, 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
•48•143•39•4•Updated Apr 16, 2025Apr 16, 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•28•3•Updated Apr 16, 2025Apr 16, 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•25•Updated Apr 16, 2025Apr 16, 2025
pathogensurveillance
Public
Surveillance of pathogens using population genomics and sequencing
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•6•22•53•2•Updated Apr 16, 2025Apr 16, 2025
nanoseq
Public
Nanopore demultiplexing, QC and alignment pipeline
workflow nanopore pipeline nextflow alignment qc demultiplexing nf-core
Nextflow
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MIT License
•93•198•50•6•Updated Apr 16, 2025Apr 16, 2025
proteinannotator
Public
The best protein annotation pipeline in the world. Protein fasta → ??? → Annotations
Nextflow
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MIT License
•3•2•10•4•Updated Apr 15, 2025Apr 15, 2025
ops
Public
Python
•2•2•29•10•Updated Apr 15, 2025Apr 15, 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
•394•121•33•12•Updated Apr 15, 2025Apr 15, 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
•303•98•9•17•Updated Apr 15, 2025Apr 15, 2025
scnanoseq
Public
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
nanopore nextflow scrna-seq single-cell 10xgenomics nf-core long-read-sequencing
Nextflow
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MIT License
•11•34•5•2•Updated Apr 15, 2025Apr 15, 2025
spatialxe
Public
Nextflow
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MIT License
•7•15•31•2•Updated Apr 15, 2025Apr 15, 2025
drop
Public
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
Nextflow
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MIT License
•1•2•0•0•Updated Apr 15, 2025Apr 15, 2025
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•6•17•5•5•Updated Apr 15, 2025Apr 15, 2025
methylong
Public
Extract methylation calls from long reads (ONT/ PacBio)
MIT License
•1•4•0•2•Updated Apr 15, 2025Apr 15, 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
•153•165•27•9•Updated Apr 15, 2025Apr 15, 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
•17•66•26•5•Updated Apr 15, 2025Apr 15, 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•10•50•4•Updated Apr 14, 2025Apr 14, 2025
hlatyping
Public
Precision HLA typing from next-generation sequencing data
workflow pipeline dna rna immunology hla personalized-medicine nf-core nextflow optitype
Nextflow
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MIT License
•31•66•11•0•Updated Apr 14, 2025Apr 14, 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 14, 2025Apr 14, 2025
ampliseq
Public
Amplicon sequencing analysis workflow using DADA2 and QIIME2
nextflow pacbio edna microbiome iontorrent illumina metabarcoding 16s rrna its
Nextflow
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MIT License
•132•198•19•3•Updated Apr 14, 2025Apr 14, 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•36•3•Updated Apr 14, 2025Apr 14, 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
•37•46•10•0•Updated Apr 14, 2025Apr 14, 2025
coproid
Public
Coprolite host Identification pipeline
workflow microbiome adna nf-core ancient-dna coprolite pipeline nextflow
Nextflow
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MIT License
•5•9•1•3•Updated Apr 14, 2025Apr 14, 2025