nf-core

All

158 repositories

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
•
MIT License
•15•3•8•0•Updated Apr 4, 2025Apr 4, 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
•
MIT License
•83•161•38•5•Updated Apr 4, 2025Apr 4, 2025
ampliseq
Public
Amplicon sequencing analysis workflow using DADA2 and QIIME2
nextflow pacbio edna microbiome iontorrent illumina metabarcoding 16s rrna its
Nextflow
•
MIT License
•131•195•19•3•Updated Apr 4, 2025Apr 4, 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
•
MIT License
•45•77•61•6•Updated Apr 4, 2025Apr 4, 2025
mag
Public
Assembly and binning of metagenomes
workflow nanopore annotation nextflow metagenomics binning nanopore-sequencing nf-core long-read-sequencing bioinformatics
Nextflow
•
MIT License
•122•232•66•12•Updated Apr 4, 2025Apr 4, 2025
methylong
Public
Extract methylation calls from long reads (ONT/ PacBio)
1•2•0•1•Updated Apr 4, 2025Apr 4, 2025
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
•
MIT License
•245•75•95•26•Updated Apr 4, 2025Apr 4, 2025
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
workflow pipeline nextflow cancer panel ngs clinical dna rna wgs
Nextflow
•
MIT License
•17•65•24•3•Updated Apr 4, 2025Apr 4, 2025
tools
Public
Python package with helper tools for the nf-core community.
bioinformatics linting linter nf-core python workflow pipeline nextflow
Python
•
MIT License
•201•253•269•32•Updated Apr 4, 2025Apr 4, 2025
proteinannotator
Public
The best protein annotation pipeline in the world. Protein fasta → ??? → Annotations
Nextflow
•
MIT License
•3•2•10•4•Updated Apr 4, 2025Apr 4, 2025
spatialxe
Public
Nextflow
•
MIT License
•7•15•28•3•Updated Apr 4, 2025Apr 4, 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
•
MIT License
•833•351•525•171•Updated Apr 3, 2025Apr 3, 2025
ops
Public
Python
•2•2•40•10•Updated Apr 3, 2025Apr 3, 2025
rnavar
Public
gatk4 RNA variant calling pipeline
workflow pipeline nextflow rnaseq rna variant-calling nf-core gatk4 worflow
Nextflow
•
MIT License
•37•46•9•1•Updated Apr 3, 2025Apr 3, 2025
epitopeprediction
Public
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
workflow nf-core epitope mhc-binding-prediction pipeline nextflow epitope-prediction
Nextflow
•
MIT License
•24•43•21•2•Updated Apr 3, 2025Apr 3, 2025
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
•
MIT License
•109•152•49•5•Updated Apr 3, 2025Apr 3, 2025
coproid
Public
Coprolite host Identification pipeline
workflow microbiome adna nf-core ancient-dna coprolite pipeline nextflow
Nextflow
•
MIT License
•5•9•1•2•Updated Apr 3, 2025Apr 3, 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
•
MIT License
•22•61•6•2•Updated Apr 3, 2025Apr 3, 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
•
MIT License
•14•29•8•0•Updated Apr 3, 2025Apr 3, 2025
pathogensurveillance
Public
Surveillance of pathogens using population genomics and sequencing
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•6•21•52•2•Updated Apr 3, 2025Apr 3, 2025
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
•
MIT License
•35•22•37•7•Updated Apr 3, 2025Apr 3, 2025
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
•
MIT License
•6•17•5•6•Updated Apr 3, 2025Apr 3, 2025
configs
Public
Config files used to define parameters specific to compute environments at different Institutions
bioinformatics nextflow configuration pipelines workflows nf-core
Nextflow
•
MIT License
•298•98•9•13•Updated Apr 2, 2025Apr 2, 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
•
MIT License
•24•54•28•3•Updated Apr 2, 2025Apr 2, 2025
lsmquant
Public
A pipeline for processing and analysis of light-sheet microscopy images.
pipeline nextflow image-processing stitching segmentation image-analysis nf-core light-sheet-microcopy 3dunet
Nextflow
•
MIT License
•1•1•0•0•Updated Apr 2, 2025Apr 2, 2025
nft-tiff
Public
A plugin to make testing of tiff files much simpler
Java
•
MIT License
•4•3•5•2•Updated Apr 2, 2025Apr 2, 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
•
MIT License
•439•438•275•42•Updated Apr 2, 2025Apr 2, 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
•390•121•33•11•Updated Apr 2, 2025Apr 2, 2025
molkart
Public
A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
fish workflow pipeline nextflow image-processing spatial segmentation transcriptomics single-cell imaging
Nextflow
•
MIT License
•11•12•9•2•Updated Apr 2, 2025Apr 2, 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
•
MIT License
•5•8•2•1•Updated Apr 2, 2025Apr 2, 2025