nf-core

All

145 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
•722•284•453•184•Updated Nov 27, 2024Nov 27, 2024
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
•146•141•36•4•Updated Nov 27, 2024Nov 27, 2024
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•5•12•9•4•Updated Nov 27, 2024Nov 27, 2024
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•196•69•90•34•Updated Nov 27, 2024Nov 27, 2024
pacvar
Public
Longread PacBio sequencing processing for WGS and PureTarget
alignment long-read pacbio variant-calling wgs puretarget
Nextflow
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MIT License
•1•1•0•2•Updated Nov 27, 2024Nov 27, 2024
nanostring
Public
An analysis pipeline for Nanostring nCounter expression data.
workflow pipeline nextflow nanostring nanostringnorm nf-core
Nextflow
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MIT License
•8•13•9•2•Updated Nov 26, 2024Nov 26, 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 26, 2024Nov 26, 2024
rnasplice
Public
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
workflow rna-seq pipeline nextflow alternative-splicing rna nf-core splicing
Nextflow
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MIT License
•27•46•9•5•Updated Nov 26, 2024Nov 26, 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
•354•106•31•11•Updated Nov 26, 2024Nov 26, 2024
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
•96•144•41•5•Updated Nov 26, 2024Nov 26, 2024
rangeland
Public
Pipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.
workflow pipeline nextflow landsat trends satellite-imagery earth-observation trend-analysis spectral-unmixing nf-core
Nextflow
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MIT License
•3•5•0•2•Updated Nov 26, 2024Nov 26, 2024
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
•35•54•20•5•Updated Nov 26, 2024Nov 26, 2024
references
Public
Nextflow
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MIT License
•4•5•9•1•Updated Nov 26, 2024Nov 26, 2024
variantbenchmarking
Public
A nextflow variant benchmarking pipeline - premature
workflow benchmark pipeline nextflow draft variant-calling structural-variants nf-core
Nextflow
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MIT License
•7•12•17•3•Updated Nov 26, 2024Nov 26, 2024
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
•30•18•15•8•Updated Nov 26, 2024Nov 26, 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
•9•3•32•5•Updated Nov 26, 2024Nov 26, 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
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MIT License
•172•214•53•4•Updated Nov 26, 2024Nov 26, 2024
proteinfold
Public
Protein 3D structure prediction pipeline
nextflow protein-structure protein-sequences protein-folding protein-fold-prediction nf-core alphafold2 workflow pipeline
Nextflow
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MIT License
•39•60•25•4•Updated Nov 26, 2024Nov 26, 2024
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
•191•242•258•36•Updated Nov 26, 2024Nov 26, 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
•37•64•58•4•Updated Nov 26, 2024Nov 26, 2024
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
•150•195•14•2•Updated Nov 26, 2024Nov 26, 2024
mhcquant
Public
Identify and quantify MHC eluted peptides from mass spectrometry raw data
workflow pipeline nextflow dda mhc mass-spectrometry openms peptides nf-core immunopeptidomics
Nextflow
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MIT License
•25•33•9•0•Updated Nov 26, 2024Nov 26, 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•50•14•3•Updated Nov 26, 2024Nov 26, 2024
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
•3•1•1•0•Updated Nov 25, 2024Nov 25, 2024
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
•34•90•32•0•Updated Nov 25, 2024Nov 25, 2024
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
•709•926•66•13•Updated Nov 25, 2024Nov 25, 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
•36•128•42•5•Updated Nov 25, 2024Nov 25, 2024
spatialxe
Public
Nextflow
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MIT License
•2•5•29•2•Updated Nov 25, 2024Nov 25, 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
•1•5•4•0•Updated Nov 25, 2024Nov 25, 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•17•12•3•Updated Nov 25, 2024Nov 25, 2024