nf-core

All

157 repositories

website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•243•74•93•33•Updated Mar 24, 2025Mar 24, 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
•767•297•527•130•Updated Mar 24, 2025Mar 24, 2025
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•6•15•5•6•Updated Mar 24, 2025Mar 24, 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
•295•96•8•11•Updated Mar 24, 2025Mar 24, 2025
proteinfold
Public
Protein 3D structure prediction pipeline
workflow pipeline nextflow protein-structure protein-sequences protein-folding protein-fold-prediction nf-core alphafold2 colabfold
Nextflow
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MIT License
•50•76•28•7•Updated Mar 24, 2025Mar 24, 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
•16•62•23•2•Updated Mar 24, 2025Mar 24, 2025
connectgame
Public
nf-core/connectgame
game nextflow nf-core
TypeScript
•56•0•0•0•Updated Mar 23, 2025Mar 23, 2025
ops
Public
Python
•2•1•40•9•Updated Mar 23, 2025Mar 23, 2025
coproid
Public
Coprolite host Identification pipeline
workflow microbiome adna nf-core ancient-dna coprolite pipeline nextflow
Nextflow
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MIT License
•4•9•2•0•Updated Mar 23, 2025Mar 23, 2025
proposals
Public
Where new ideas for nf-core pipelines and more are proposed
MIT License
•0•1•1•0•Updated Mar 23, 2025Mar 23, 2025
stats
Public
evidence
HTML
•2•0•13•10•Updated Mar 22, 2025Mar 22, 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
•198•252•256•31•Updated Mar 22, 2025Mar 22, 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
•43•97•36•3•Updated Mar 21, 2025Mar 21, 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
•37•44•13•1•Updated Mar 21, 2025Mar 21, 2025
clipseq
Public
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
workflow clip-seq nf-core peak-calling rna-rbp-interactions pipeline nextflow clip
Nextflow
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MIT License
•30•21•28•3•Updated Mar 21, 2025Mar 21, 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
•741•999•81•15•Updated Mar 21, 2025Mar 21, 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•21•14•1•Updated Mar 21, 2025Mar 21, 2025
variantbenchmarking
Public
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
workflow benchmark pipeline nextflow draft variant-calling structural-variants nf-core
Nextflow
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MIT License
•12•26•15•0•Updated Mar 21, 2025Mar 21, 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•160•36•6•Updated Mar 21, 2025Mar 21, 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
•119•133•31•4•Updated Mar 21, 2025Mar 21, 2025
proteinfamilies
Public
Generation and update of protein families
workflow bioinformatics pipeline nextflow metagenomics proteomics protein-families nf-core
Nextflow
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MIT License
•1•9•14•0•Updated Mar 21, 2025Mar 21, 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
•44•74•62•5•Updated Mar 20, 2025Mar 20, 2025
lncpipe
Public
UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
workflow pipeline nextflow rna transcriptome rna-seq-analysis differential-expression lncrna non-coding nf-core
Nextflow
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MIT License
•44•34•26•0•Updated Mar 20, 2025Mar 20, 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
•368•117•31•10•Updated Mar 20, 2025Mar 20, 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•9•30•6•Updated Mar 20, 2025Mar 20, 2025
nft-tiff
Public
A plugin to make testing of tiff files much simpler
Java
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MIT License
•4•1•0•1•Updated Mar 20, 2025Mar 20, 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
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MIT License
•106•150•47•6•Updated Mar 20, 2025Mar 20, 2025
cutandrun
Public
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
workflow pipeline nextflow nf-core cutandrun-seq cutandrun cutandtag-seq cutandtag
Nextflow
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MIT License
•50•89•30•6•Updated Mar 20, 2025Mar 20, 2025
fetchngs
Public
Pipeline to fetch metadata and raw FastQ files from public databases
workflow pipeline nextflow download geo fastq synapse sra ena nf-core
Nextflow
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MIT License
•80•171•27•11•Updated Mar 19, 2025Mar 19, 2025
genomeassembler
Public
Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
workflow pipeline nextflow genome-assembly nf-core
Nextflow
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MIT License
•13•19•3•0•Updated Mar 19, 2025Mar 19, 2025