nf-core

All

158 repositories

website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•245•75•94•25•Updated Apr 13, 2025Apr 13, 2025
ops
Public
Python
•2•2•29•10•Updated Apr 12, 2025Apr 12, 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
•24•54•30•4•Updated Apr 12, 2025Apr 12, 2025
reportho
Public
nf-core pipeline for comparative analysis of ortholog predictions
Nextflow
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MIT License
•6•11•6•2•Updated Apr 12, 2025Apr 12, 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
•836•352•512•176•Updated Apr 12, 2025Apr 12, 2025
methylarray
Public
Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.
Nextflow
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MIT License
•3•4•12•1•Updated Apr 12, 2025Apr 12, 2025
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
•153•165•26•8•Updated Apr 12, 2025Apr 12, 2025
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
workflow pipeline nextflow cancer panel ngs clinical dna rna wgs
Nextflow
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MIT License
•17•65•27•6•Updated Apr 11, 2025Apr 11, 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
•13•23•11•0•Updated Apr 11, 2025Apr 11, 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
•392•121•33•13•Updated Apr 11, 2025Apr 11, 2025
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
•748•1k•86•15•Updated Apr 11, 2025Apr 11, 2025
references
Public
nf-core/references is a bioinformatics pipeline that build references, for multiple use cases
genome reproducible-research reproducible-science references reproducibility
Nextflow
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MIT License
•5•14•23•3•Updated Apr 11, 2025Apr 11, 2025
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
•8•9•5•1•Updated Apr 11, 2025Apr 11, 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
•23•83•16•0•Updated Apr 11, 2025Apr 11, 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
•301•98•9•15•Updated Apr 11, 2025Apr 11, 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
•44•99•36•5•Updated Apr 11, 2025Apr 11, 2025
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
•439•439•280•41•Updated Apr 11, 2025Apr 11, 2025
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
•16•10•47•4•Updated Apr 11, 2025Apr 11, 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
•22•61•5•1•Updated Apr 11, 2025Apr 11, 2025
eager
Public
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
workflow metagenomics population-genetics adna pathogen-genomics nf-core ancientdna bioinformatics pipeline genome
Nextflow
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MIT License
•83•161•38•4•Updated Apr 11, 2025Apr 11, 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
•15•4•6•0•Updated Apr 11, 2025Apr 11, 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
•48•143•42•6•Updated Apr 11, 2025Apr 11, 2025
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•6•17•5•6•Updated Apr 11, 2025Apr 11, 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
•7•9•10•1•Updated Apr 11, 2025Apr 11, 2025
hlatyping
Public
Precision HLA typing from next-generation sequencing data
workflow pipeline dna rna immunology hla personalized-medicine nf-core nextflow optitype
Nextflow
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MIT License
•31•65•13•2•Updated Apr 11, 2025Apr 11, 2025
pathogensurveillance
Public
Surveillance of pathogens using population genomics and sequencing
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•6•22•53•2•Updated Apr 10, 2025Apr 10, 2025
methylong
Public
Extract methylation calls from long reads (ONT/ PacBio)
MIT License
•1•3•0•2•Updated Apr 10, 2025Apr 10, 2025
smrnaseq
Public
A small-RNA sequencing analysis pipeline
workflow pipeline nextflow small-rna nf-core smrna-seq
Nextflow
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MIT License
•127•83•14•2•Updated Apr 10, 2025Apr 10, 2025
viralrecon
Public
Assembly and intrahost/low-frequency variant calling for viral samples
workflow nanopore virus pipeline nextflow assembly metagenomics variant-calling illumina oxford-nanopore
Nextflow
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MIT License
•127•135•28•10•Updated Apr 10, 2025Apr 10, 2025
metatdenovo
Public
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
workflow pipeline nextflow metagenomics viruses metatranscriptomics prokaryotes eukaryotes nf-core
Nextflow
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MIT License
•14•29•9•1•Updated Apr 10, 2025Apr 10, 2025