nf-core

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150 repositories

ops
Public
Python
•2•1•48•8•Updated Jan 10, 2025Jan 10, 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
•6•22•1•1•Updated Jan 10, 2025Jan 10, 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
•
MIT License
•37•55•20•4•Updated Jan 10, 2025Jan 10, 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
•737•288•464•185•Updated Jan 10, 2025Jan 10, 2025
atacseq
Public
ATAC-seq peak-calling and QC analysis pipeline
workflow pipeline nextflow atac-seq nf-core chromatin-accessibiity
Nextflow
•
MIT License
•123•195•34•3•Updated Jan 10, 2025Jan 10, 2025
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•194•70•90•41•Updated Jan 10, 2025Jan 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
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MIT License
•37•92•33•3•Updated Jan 10, 2025Jan 10, 2025
proteinfamilies
Public
Generation and update of protein families
workflow bioinformatics pipeline nextflow metagenomics proteomics protein-families nf-core
Nextflow
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MIT License
•1•2•0•1•Updated Jan 10, 2025Jan 10, 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
•34•40•37•3•Updated Jan 10, 2025Jan 10, 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
•38•133•39•7•Updated Jan 10, 2025Jan 10, 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
•20•53•5•1•Updated Jan 10, 2025Jan 10, 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
•22•77•16•4•Updated Jan 10, 2025Jan 10, 2025
references-assets
Public
Shell
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MIT License
•1•0•0•0•Updated Jan 10, 2025Jan 10, 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
•5•1•1•0•Updated Jan 10, 2025Jan 10, 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
•279•91•12•17•Updated Jan 10, 2025Jan 10, 2025
chipseq
Public
ChIP-seq peak-calling, QC and differential analysis pipeline.
workflow chip nf-core peak-calling pipeline nextflow chip-seq macs2 chromatin-immunoprecipitation
Nextflow
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MIT License
•149•204•16•2•Updated Jan 10, 2025Jan 10, 2025
denovotranscript
Public
A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq
rna-seq transcriptome denovo-assembly
Nextflow
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MIT License
•4•11•4•0•Updated Jan 10, 2025Jan 10, 2025
scdownstream
Public
A single cell transcriptomics pipeline for QC, integration and making the data presentable
quality-control integration clustering dimensionality-reduction single-cell scverse
Nextflow
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MIT License
•15•45•25•3•Updated Jan 10, 2025Jan 10, 2025
mcmicro
Public
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
workflow pipeline nextflow image-processing spatial stitching registration segmentation image-analysis single-cell
Nextflow
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MIT License
•16•8•23•4•Updated Jan 9, 2025Jan 9, 2025
stats
Public
evidence
HTML
•0•0•13•10•Updated Jan 9, 2025Jan 9, 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
•192•245•275•36•Updated Jan 9, 2025Jan 9, 2025
references
Public
Nextflow
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MIT License
•4•11•14•0•Updated Jan 9, 2025Jan 9, 2025
mag
Public
Assembly and binning of metagenomes
workflow nanopore annotation nextflow metagenomics binning nanopore-sequencing nf-core long-read-sequencing bioinformatics
Nextflow
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MIT License
•114•223•63•10•Updated Jan 9, 2025Jan 9, 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
•6•7•14•2•Updated Jan 9, 2025Jan 9, 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
•99•148•41•3•Updated Jan 9, 2025Jan 9, 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
•4•8•0•1•Updated Jan 9, 2025Jan 9, 2025
logos
Public
Host nf-core logos and templates for making new logos
nextflow logo nf-core
MIT License
•10•4•0•0•Updated Jan 9, 2025Jan 9, 2025
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•6•14•8•6•Updated Jan 9, 2025Jan 9, 2025
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•10•57•14•3•Updated Jan 9, 2025Jan 9, 2025
isoseq
Public
Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
workflow pipeline nextflow rna ultra nf-core tama isoseq-3 isoseq
Nextflow
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MIT License
•16•31•6•2•Updated Jan 9, 2025Jan 9, 2025