nf-core

All

142 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
•712•280•449•167•Updated Oct 31, 2024Oct 31, 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
•36•44•19•1•Updated Oct 31, 2024Oct 31, 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
•189•241•250•36•Updated Oct 31, 2024Oct 31, 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
•2•3•3•1•Updated Oct 31, 2024Oct 31, 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
•350•105•31•9•Updated Oct 31, 2024Oct 31, 2024
ops
Public
Python
•2•1•23•10•Updated Oct 31, 2024Oct 31, 2024
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•4•12•8•4•Updated Oct 31, 2024Oct 31, 2024
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•192•67•89•34•Updated Oct 31, 2024Oct 31, 2024
pathogensurveillance
Public
Surveillance of pathogens using population genomics and sequencing
workflow pipeline nextflow nf-core
HTML
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MIT License
•5•12•43•0•Updated Oct 30, 2024Oct 30, 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•43•12•2•Updated Oct 30, 2024Oct 30, 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•12•1•Updated Oct 30, 2024Oct 30, 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•7•14•2•Updated Oct 30, 2024Oct 30, 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•10•0•Updated Oct 30, 2024Oct 30, 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
•36•61•53•9•Updated Oct 30, 2024Oct 30, 2024
fastqrepair
Public
A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered
corruption fastq-format fastq data-cleaning data-recovery well-formed recovery-tool fastq-corrupted unpaired-reads reads-interleaving
Nextflow
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MIT License
•1•0•1•1•Updated Oct 30, 2024Oct 30, 2024
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
•20•73•15•1•Updated Oct 30, 2024Oct 30, 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
•271•87•11•10•Updated Oct 30, 2024Oct 30, 2024
nft-tiff
Public
A plugin to make testing of tiff files much simpler
Java
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MIT License
•2•0•0•0•Updated Oct 30, 2024Oct 30, 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
•169•211•54•4•Updated Oct 30, 2024Oct 30, 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•37•31•1•Updated Oct 30, 2024Oct 30, 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 Oct 30, 2024Oct 30, 2024
seqinspector
Public
QC pipeline to inspect your sequences
workflow quality-control pipeline genomics nextflow nf-core
Nextflow
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MIT License
•20•4•29•9•Updated Oct 30, 2024Oct 30, 2024
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
•407•404•256•33•Updated Oct 30, 2024Oct 30, 2024
tbanalyzer
Public
An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.
workflow pipeline nextflow reproducible-research mycobacterium-tuberculosis-complex nf-core mycobacterium-tuberculosis
Nextflow
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MIT License
•1•7•1•1•Updated Oct 30, 2024Oct 30, 2024
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
•110•213•58•7•Updated Oct 30, 2024Oct 30, 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 Oct 30, 2024Oct 30, 2024
actions-runners
Public
Instructions and scripts for custom GitHub Actions runners
Shell
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MIT License
•3•2•1•0•Updated Oct 30, 2024Oct 30, 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•19•1•Updated Oct 30, 2024Oct 30, 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
•144•140•29•4•Updated Oct 30, 2024Oct 30, 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•29•7•Updated Oct 29, 2024Oct 29, 2024