nf-core

All

150 repositories

setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•6•14•8•4•Updated Jan 17, 2025Jan 17, 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•1•Updated Jan 16, 2025Jan 16, 2025
circrna
Public
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
workflow pipeline genomics nextflow ngs circrna mirna circular-rna circrna-prediction mirna-targets
Nextflow
•
MIT License
•26•48•16•5•Updated Jan 16, 2025Jan 16, 2025
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•200•70•91•32•Updated Jan 16, 2025Jan 16, 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
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MIT License
•739•290•464•185•Updated Jan 16, 2025Jan 16, 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
•363•110•31•16•Updated Jan 16, 2025Jan 16, 2025
ops
Public
Python
•2•1•48•8•Updated Jan 16, 2025Jan 16, 2025
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
•177•224•53•2•Updated Jan 16, 2025Jan 16, 2025
genomeassembler
Public
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•13•16•37•2•Updated Jan 16, 2025Jan 16, 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•14•2•Updated Jan 16, 2025Jan 16, 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 16, 2025Jan 16, 2025
pangenome
Public
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
workflow pipeline nextflow pangenome nf-core
Nextflow
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MIT License
•18•80•12•0•Updated Jan 16, 2025Jan 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
•192•245•271•34•Updated Jan 16, 2025Jan 16, 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•93•34•2•Updated Jan 16, 2025Jan 16, 2025
meerpipe
Public
nf-core/meerpipe is a astronomy pipeline that processes MeerKAT pulsar data to produce images and data products for pulsar timing analysis
Nextflow
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MIT License
•4•7•0•1•Updated Jan 16, 2025Jan 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
•41•68•75•7•Updated Jan 15, 2025Jan 15, 2025
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
•2•1•5•1•Updated Jan 15, 2025Jan 15, 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•2•Updated Jan 15, 2025Jan 15, 2025
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
•8•14•17•1•Updated Jan 15, 2025Jan 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
•281•91•12•14•Updated Jan 15, 2025Jan 15, 2025
seqinspector
Public
QC pipeline to inspect your sequences
workflow quality-control pipeline genomics nextflow nf-core
Nextflow
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MIT License
•22•7•26•9•Updated Jan 15, 2025Jan 15, 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•36•2•Updated Jan 15, 2025Jan 15, 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•134•39•6•Updated Jan 15, 2025Jan 15, 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
•115•225•64•10•Updated Jan 15, 2025Jan 15, 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•32•6•1•Updated Jan 15, 2025Jan 15, 2025
pathogensurveillance
Public
Surveillance of pathogens using population genomics and sequencing
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•6•14•43•0•Updated Jan 14, 2025Jan 14, 2025
fastquorum
Public
Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
workflow pipeline nextflow consensus umi unique-molecular-identifier nf-core umis
Nextflow
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MIT License
•11•20•14•2•Updated Jan 14, 2025Jan 14, 2025
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
•27•33•12•0•Updated Jan 14, 2025Jan 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
•123•190•27•3•Updated Jan 14, 2025Jan 14, 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 14, 2025Jan 14, 2025