nf-core

All

143 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
•715•280•449•157•Updated Nov 5, 2024Nov 5, 2024
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
•10•18•37•4•Updated Nov 5, 2024Nov 5, 2024
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•8•46•13•2•Updated Nov 5, 2024Nov 5, 2024
modules-template
Public
Nextflow
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MIT License
•1•0•0•1•Updated Nov 5, 2024Nov 5, 2024
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
•3•3•3•1•Updated Nov 5, 2024Nov 5, 2024
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•193•68•89•35•Updated Nov 5, 2024Nov 5, 2024
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
•34•128•42•6•Updated Nov 5, 2024Nov 5, 2024
scrnaseq
Public
A single-cell RNAseq pipeline for 10X genomics data
workflow rna-seq pipeline nextflow single-cell kallisto 10x-genomics 10xgenomics nf-core bustools
Nextflow
•
MIT License
•170•212•54•6•Updated Nov 5, 2024Nov 5, 2024
deepmodeloptim
Public
Stochastic Testing and Input Manipulation for Unbiased Learning Systems
genomics optimization artificial-intelligence deeplearning large-scale dataprocessing prototyping-tool
Nextflow
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MIT License
•9•23•23•0•Updated Nov 5, 2024Nov 5, 2024
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
•8•1•33•6•Updated Nov 5, 2024Nov 5, 2024
magmap
Public
Nextflow
•
MIT License
•4•3•9•4•Updated Nov 5, 2024Nov 5, 2024
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•5•12•8•3•Updated Nov 5, 2024Nov 5, 2024
tfactivity
Public
Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
workflow transcription-factors pipeline nextflow transcriptomics nf-core open-chromatin-regions
Nextflow
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MIT License
•3•9•3•3•Updated Nov 5, 2024Nov 5, 2024
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
•12•38•27•1•Updated Nov 5, 2024Nov 5, 2024
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
•35•62•54•7•Updated Nov 5, 2024Nov 5, 2024
demultiplex
Public
Demultiplexing pipeline for sequencing data
nextflow illumina demultiplexing bcl2fastq nf-core bases2fastq elementbiosciences workflow pipeline
Nextflow
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MIT License
•37•44•17•1•Updated Nov 5, 2024Nov 5, 2024
bacass
Public
Simple bacterial assembly and annotation pipeline
workflow denovo genome-assembly denovo-assembly bacterial-genomes nanopore-sequencing nf-core nanopore pipeline nextflow
Nextflow
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MIT License
•41•60•16•2•Updated Nov 5, 2024Nov 5, 2024
nft-tiff
Public
A plugin to make testing of tiff files much simpler
Java
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MIT License
•2•0•0•1•Updated Nov 5, 2024Nov 5, 2024
setup-nf-test
Public
JavaScript
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MIT License
•2•2•0•0•Updated Nov 5, 2024Nov 5, 2024
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
•272•87•11•12•Updated Nov 5, 2024Nov 5, 2024
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
•352•105•31•9•Updated Nov 5, 2024Nov 5, 2024
fetchngs
Public
Pipeline to fetch metadata and raw FastQ files from public databases
workflow pipeline nextflow download geo fastq synapse sra ena nf-core
Nextflow
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MIT License
•73•150•21•5•Updated Nov 5, 2024Nov 5, 2024
metapep
Public
From metagenomes to epitopes and beyond
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•5•8•12•2•Updated Nov 5, 2024Nov 5, 2024
phaseimpute
Public
A bioinformatics pipeline to phase and impute genetic data
pipeline genomics imputation genotype phasing low-pass-sequencing
Nextflow
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MIT License
•14•16•13•4•Updated Nov 5, 2024Nov 5, 2024
createpanelrefs
Public
Generate Panel of Normals, models or other similar references from lots of samples
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•7•7•7•1•Updated Nov 4, 2024Nov 4, 2024
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
•15•8•23•4•Updated Nov 4, 2024Nov 4, 2024
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
•6•9•15•1•Updated Nov 4, 2024Nov 4, 2024
ops
Public
Python
•2•1•23•9•Updated Nov 4, 2024Nov 4, 2024
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
•0•4•4•1•Updated Nov 4, 2024Nov 4, 2024
detaxizer
Public
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
workflow nanopore pipeline nextflow shotgun filter metagenomics edna microbiome fastq
Nextflow
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MIT License
•5•14•1•1•Updated Nov 4, 2024Nov 4, 2024