Repositories list

• website

  Public

  nf-core/website’s past year of commit activity
  Code and files for the main nf-core website.

  websitenextflownf-core

  MDX

  •

  MIT License

  •261•85•115•30•Updated Feb 5, 2026Feb 5, 2026

• ops

  Public

  nf-core/ops’s past year of commit activity
  Different *Ops related scripts for the nf-core org.

  Python

  •2•3•37•19•Updated Feb 5, 2026Feb 5, 2026

• setup-nextflow

  Public

  nf-core/setup-nextflow’s past year of commit activity
  A GitHub action to install Nextflow

  nextflowactions

  TypeScript

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  MIT License

  •4•26•6•11•Updated Feb 5, 2026Feb 5, 2026

• rnaseq

  Public

  nf-core/rnaseq’s past year of commit activity
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

  workflowrna-seqpipeline+ 3nextflowrnanf-core

  Nextflow

  •

  MIT License

  •842•1.2k•33•14•Updated Feb 5, 2026Feb 5, 2026

• variantprioritization

  Public

  nf-core/variantprioritization’s past year of commit activity
  Analysis pipeline for the functional annotation and translation of somatic SNVs/InDels and copy number abberations for precision cancer medicine.

  workflowpipelinenextflow+ 1nf-core

  Nextflow

  •

  MIT License

  •9•12•11•2•Updated Feb 5, 2026Feb 5, 2026

• modules

  Public

  nf-core/modules’s past year of commit activity
  Repository to host tool-specific module files for the Nextflow DSL2 community!

  modulesnextflowpipelines+ 4workflowsnf-coredsl2nf-test

  Nextflow

  •

  MIT License

  •962•394•378•165•Updated Feb 5, 2026Feb 5, 2026

• variantbenchmarking

  Public

  nf-core/variantbenchmarking’s past year of commit activity
  Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research

  workflowbenchmarkpipeline+ 5nextflowvariant-callingstructural-variantsnf-coresmall-variants

  Nextflow

  •

  MIT License

  •21•38•26•1•Updated Feb 5, 2026Feb 5, 2026

• demultiplex

  Public

  nf-core/demultiplex’s past year of commit activity
  Demultiplexing pipeline for sequencing data

  workflowpipelinenextflow+ 6illuminademultiplexingbcl2fastqnf-corebases2fastqelementbiosciences

  Nextflow

  •

  MIT License

  •50•52•25•0•Updated Feb 5, 2026Feb 5, 2026

• sopa

  Public

  nf-core/sopa’s past year of commit activity
  Nextflow version of Sopa - spatial omics pipeline and analysis

  workflowpipelinenextflow+ 6segmentationspatial-proteomicsnf-corespatial-transcriptomicsspatialdataspatial-omics

  Nextflow

  •

  MIT License

  •4•13•1•2•Updated Feb 5, 2026Feb 5, 2026

• proteinfold

  Public

  nf-core/proteinfold’s past year of commit activity
  Protein 3D structure prediction pipeline

  workflowpipelinenextflow+ 8protein-structureprotein-sequencesprotein-foldingprotein-fold-predictionnf-corealphafold2colabfold+ 1

  HTML

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  MIT License

  •61•97•50•7•Updated Feb 5, 2026Feb 5, 2026

• mcmicro

  Public

  nf-core/mcmicro’s past year of commit activity
  An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

  workflowpipelinenextflow+ 13image-processingspatialstitchingregistrationsegmentationimage-analysissingle-cell+ 6

  Nextflow

  •

  MIT License

  •20•30•36•6•Updated Feb 5, 2026Feb 5, 2026

• phaseimpute

  Public

  nf-core/phaseimpute’s past year of commit activity
  A bioinformatics pipeline to phase and impute genetic data

  workflowpipelinegenomics+ 5nextflowimputationgenotypephasinglow-pass-sequencing

  Nextflow

  •

  MIT License

  •20•27•17•6•Updated Feb 5, 2026Feb 5, 2026

• cageseq

  Public

  nf-core/cageseq’s past year of commit activity
  CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

  workflowpipelinenextflow+ 6gene-expressionrnacagenf-corecage-seqcageseq-data

  Nextflow

  •

  MIT License

  •12•11•3•5•Updated Feb 5, 2026Feb 5, 2026

• test-datasets

  Public

  nf-core/test-datasets’s past year of commit activity
  Test data to be used for automated testing with the nf-core pipelines

  testingworkflownextflow+ 4pipelinestest-datatest-datasetsnf-core

  MIT License

  •459•150•35•20•Updated Feb 5, 2026Feb 5, 2026

• sarek

  Public

  nf-core/sarek’s past year of commit activity
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

  workflowbioinformaticspipeline+ 17annotationgenomicsnextflowcancerreproducible-researchcontainersconda+ 10

  Nextflow

  •

  MIT License

  •517•542•303•40•Updated Feb 5, 2026Feb 5, 2026

• epitopeprediction

  Public

  nf-core/epitopeprediction’s past year of commit activity
  A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

  workflowpipelinenextflow+ 4epitope-predictionnf-coreepitopemhc-binding-prediction

  Nextflow

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  MIT License

  •30•51•15•2•Updated Feb 5, 2026Feb 5, 2026

• createpanelrefs

  Public

  nf-core/createpanelrefs’s past year of commit activity
  Generate Panel of Normals, models or other similar references from lots of samples

  workflowpipelinenextflow+ 1nf-core

  Nextflow

  •

  MIT License

  •11•10•8•3•Updated Feb 5, 2026Feb 5, 2026

• spatialvi

  Public

  nf-core/spatialvi’s past year of commit activity
  Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

  workflowbioinformaticsrna-seq+ 13pipelinenextflowimage-processingspatialtranscriptomicssingle-cellmicroscopy+ 6

  Nextflow

  •

  MIT License

  •30•70•2•1•Updated Feb 5, 2026Feb 5, 2026

• proteinannotator

  Public

  nf-core/proteinannotator’s past year of commit activity
  Generation of sequence-level annotations for amino acid sequences

  workflowpipelineannotation+ 3nextflowproteomicsnf-core

  Nextflow

  •

  MIT License

  •9•9•20•6•Updated Feb 5, 2026Feb 5, 2026

• oncoanalyser

  Public
  A comprehensive cancer DNA/RNA analysis and reporting pipeline

  workflowpipelinenextflow+ 14cancerpanelngsclinicaldnarnawgs+ 7

  Nextflow

  •

  MIT License

  •27•101•10•6•Updated Feb 5, 2026Feb 5, 2026

• coproid

  Public

  nf-core/coproid’s past year of commit activity
  Coprolite host Identification pipeline

  workflowpipelinenextflow+ 5microbiomeadnanf-coreancient-dnacoprolite

  Nextflow

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  MIT License

  •4•12•1•4•Updated Feb 5, 2026Feb 5, 2026

• strict-syntax-health

  Public

  nf-core/strict-syntax-health’s past year of commit activity
  Track Nextflow strict syntax linting health across nf-core pipelines

  Python

  •

  MIT License

  •1•6•0•0•Updated Feb 5, 2026Feb 5, 2026

• raredisease

  Public

  nf-core/raredisease’s past year of commit activity
  Call and score variants from WGS/WES of rare disease patients.

  workflowpipelinenextflow+ 9diagnosticsvariant-callingwgssnvwesvariant-annotationstructural-variants+ 2

  Nextflow

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  MIT License

  •57•112•49•4•Updated Feb 4, 2026Feb 4, 2026

• cellpainting

  Public

  nf-core/cellpainting’s past year of commit activity
  workflowpipelinenextflow+ 1nf-core

  Nextflow

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  MIT License

  •6•7•14•4•Updated Feb 4, 2026Feb 4, 2026

• crisprseq

  Public
  A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing…

  workflowpipelinenextflow+ 5ngscrispr-analysiscrisprnf-corecrispr-cas

  Nextflow

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  MIT License

  •31•52•25•4•Updated Feb 4, 2026Feb 4, 2026

• lsmquant

  Public

  nf-core/lsmquant’s past year of commit activity
  A pipeline for processing and analysis of light-sheet microscopy images.

  pipelinenextflowimage-processing+ 6stitchingsegmentationimage-analysisnf-corelight-sheet-microcopy3dunet

  Nextflow

  •

  MIT License

  •1•5•0•2•Updated Feb 4, 2026Feb 4, 2026

• configs

  Public
  Config files used to define parameters specific to compute environments at different Institutions

  bioinformaticsnextflowconfiguration+ 3pipelinesworkflowsnf-core

  Nextflow

  •

  MIT License

  •339•107•10•16•Updated Feb 4, 2026Feb 4, 2026

• tools

  Public
  Python package with helper tools for the nf-core community.

  pythonworkflowbioinformatics+ 5pipelinenextflowlintinglinternf-core

  Python

  •

  MIT License

  •224•290•330•46•Updated Feb 4, 2026Feb 4, 2026

• scdownstream

  Public

  nf-core/scdownstream’s past year of commit activity
  A single cell transcriptomics pipeline for QC, integration and making the data presentable

  workflowquality-controlintegration+ 7pipelinenextflowclusteringdimensionality-reductionsingle-cellnf-corescverse

  Nextflow

  •

  MIT License

  •51•83•37•2•Updated Feb 3, 2026Feb 3, 2026

• hlatyping

  Public
  Precision HLA typing from next-generation sequencing data

  workflowpipelinenextflow+ 8dnarnaimmunologyhlaoptitypehla-typingpersonalized-medicine+ 1

  Nextflow

  •

  MIT License

  •34•78•11•2•Updated Feb 3, 2026Feb 3, 2026