nf-core

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157 repositories

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•3•1•Updated Mar 25, 2025Mar 25, 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
•798•297•551•149•Updated Mar 24, 2025Mar 24, 2025
pacvar
Public
Longread PacBio sequencing processing for WGS and PureTarget
alignment long-read pacbio variant-calling wgs puretarget
Nextflow
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MIT License
•6•8•4•2•Updated Mar 24, 2025Mar 24, 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
•37•21•33•5•Updated Mar 24, 2025Mar 24, 2025
bactmap
Public
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
workflow tree pipeline genomics mapping bacteria bacterial nf-core bacterial-genome-analysis nextflow
Nextflow
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MIT License
•47•53•38•3•Updated Mar 24, 2025Mar 24, 2025
airrflow
Public
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
nextflow nf-core b-cell repseq immcantation immunorepertoire airr workflow pipeline
Nextflow
•
MIT License
•40•58•23•4•Updated Mar 24, 2025Mar 24, 2025
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•242•74•95•30•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
proteinannotator
Public
The best protein annotation pipeline in the world. Protein fasta → ??? → Annotations
Nextflow
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MIT License
•1•1•9•1•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•24•2•Updated Mar 24, 2025Mar 24, 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
•5•8•0•1•Updated Mar 24, 2025Mar 24, 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
•200•252•259•34•Updated Mar 24, 2025Mar 24, 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
•436•432•275•38•Updated Mar 24, 2025Mar 24, 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•97•37•3•Updated Mar 24, 2025Mar 24, 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•37•6•Updated Mar 24, 2025Mar 24, 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
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MIT License
•11•11•10•2•Updated Mar 24, 2025Mar 24, 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
•125•133•31•5•Updated Mar 24, 2025Mar 24, 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
•130•195•36•4•Updated Mar 24, 2025Mar 24, 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
•151•160•27•8•Updated Mar 24, 2025Mar 24, 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
•371•117•31•11•Updated Mar 24, 2025Mar 24, 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
•14•2•11•0•Updated Mar 24, 2025Mar 24, 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•11•15•1•Updated Mar 24, 2025Mar 24, 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
•48•34•25•1•Updated Mar 24, 2025Mar 24, 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•16•0•Updated Mar 24, 2025Mar 24, 2025
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
•12•26•22•1•Updated Mar 24, 2025Mar 24, 2025
nanoseq
Public
Nanopore demultiplexing, QC and alignment pipeline
workflow nanopore pipeline nextflow alignment qc demultiplexing nf-core
Nextflow
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MIT License
•91•194•51•5•Updated Mar 24, 2025Mar 24, 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
•47•139•41•5•Updated Mar 24, 2025Mar 24, 2025
ops
Public
Python
•2•1•40•9•Updated Mar 24, 2025Mar 24, 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
•4•11•23•1•Updated Mar 24, 2025Mar 24, 2025
demo
Public
nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.
training workflow demo tutorial pipeline minimal-example nf-core
Nextflow
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MIT License
•8•3•4•1•Updated Mar 24, 2025Mar 24, 2025