Repositories list

• website

  Public

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

  websitenextflownf-core

  websitenextflownf-core

  MDX

  •

  MIT License

  •287287 forks•9191 stars•119119 issues•3131 pull requests•Updated Apr 19, 2026Apr 19, 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+ 3

  workflowrna-seqpipelinenextflowrnanf-core

  Nextflow

  •

  MIT License

  •860860 forks•1.3k1.3k stars•2525 issues•1212 pull requests•Updated Apr 19, 2026Apr 19, 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+ 4

  modulesnextflowpipelinesworkflowsnf-coredsl2nf-test

  Nextflow

  •

  MIT License

  •1k1k forks•411411 stars•307307 issues•178178 pull requests•Updated Apr 19, 2026Apr 19, 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

  •44 forks•77 stars•00 issues•00 pull requests•Updated Apr 19, 2026Apr 19, 2026

• diseasemodulediscovery

  Public

  nf-core/diseasemodulediscovery’s past year of commit activity
  A pipeline for network-based disease module identification.

  pipelinenextflowsystems-biology+ 13

  pipelinenextflowsystems-biologydrug-repurposingnetworksprotein-protein-interactionnf-coreprotein-protein-interaction-networkdisease-modulesdisease-mechanisms+ 6

  Python

  •

  MIT License

  •44 forks•55 stars•3737 issues•88 pull requests•Updated Apr 18, 2026Apr 18, 2026

• funcprofiler

  Public

  nf-core/funcprofiler’s past year of commit activity
  Read-based functional profiling of microbiome sequencing data

  workflowpipelinenextflow+ 1

  workflowpipelinenextflownf-core

  Nextflow

  •

  MIT License

  •33 forks•22 stars•1212 issues•22 pull requests•Updated Apr 18, 2026Apr 18, 2026

• setup-nf-test

  Public

  nf-core/setup-nf-test’s past year of commit activity
  JavaScript

  •

  MIT License

  •33 forks•77 stars•11 issue•33 pull requests•Updated Apr 18, 2026Apr 18, 2026

• ops

  Public

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

  Python

  •33 forks•33 stars•3737 issues•2020 pull requests•Updated Apr 18, 2026Apr 18, 2026

• magmap

  Public

  nf-core/magmap’s past year of commit activity
  Best-practice analysis pipeline for mapping reads to a (large) collections of genomes

  workflowpipelinenextflow+ 1

  workflowpipelinenextflownf-core

  Nextflow

  •

  MIT License

  •66 forks•1010 stars•66 issues•11 pull request•Updated Apr 18, 2026Apr 18, 2026

• tools

  Public

  nf-core/tools’s past year of commit activity
  Python package with helper tools for the nf-core community.

  pythonworkflowbioinformatics+ 5

  pythonworkflowbioinformaticspipelinenextflowlintinglinternf-core

  Python

  •

  MIT License

  •238238 forks•300300 stars•329329 issues•4848 pull requests•Updated Apr 17, 2026Apr 17, 2026

• configs

  Public

  nf-core/configs’s past year of commit activity
  Config files used to define parameters specific to compute environments at different Institutions

  bioinformaticsnextflowconfiguration+ 3

  bioinformaticsnextflowconfigurationpipelinesworkflowsnf-core

  Nextflow

  •

  MIT License

  •353353 forks•108108 stars•1212 issues•2929 pull requests•Updated Apr 17, 2026Apr 17, 2026

• seqinspector

  Public

  nf-core/seqinspector’s past year of commit activity
  Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc rep…

  workflowquality-controlpipeline+ 3

  workflowquality-controlpipelinegenomicsnextflownf-core

  Nextflow

  •

  MIT License

  •4040 forks•2424 stars•2626 issues•33 pull requests•Updated Apr 17, 2026Apr 17, 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+ 17

  workflowbioinformaticspipelineannotationgenomicsnextflowcancerreproducible-researchcontainersconda+ 10

  Nextflow

  •

  MIT License

  •526526 forks•559559 stars•238238 issues•3838 pull requests•Updated Apr 17, 2026Apr 17, 2026

• spatialvi

  Public
  Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

  workflowbioinformaticsrna-seq+ 13

  workflowbioinformaticsrna-seqpipelinenextflowimage-processingspatialtranscriptomicssingle-cellmicroscopy+ 6

  Nextflow

  •

  MIT License

  •3535 forks•7272 stars•11 issue•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• stableexpression

  Public

  nf-core/stableexpression’s past year of commit activity
  This pipeline is dedicated to identifying the most stable genes within a single or multiple expression dataset(s). This is particularly useful for identifying t…

  workflowpipelinenextflow+ 4

  workflowpipelinenextflowexpressionnf-corehousekeeping-genesqpcr-analysis

  Python

  •

  MIT License

  •11 fork•88 stars•00 issues•22 pull requests•Updated Apr 17, 2026Apr 17, 2026

• demultiplex

  Public
  Demultiplexing pipeline for sequencing data

  workflowpipelinenextflow+ 6

  workflowpipelinenextflowilluminademultiplexingbcl2fastqnf-corebases2fastqelementbiosciences

  Nextflow

  •

  MIT License

  •5252 forks•5454 stars•1515 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• ampliseq

  Public
  Amplicon sequencing analysis workflow using DADA2 and QIIME2

  workflowpipelinenextflow+ 17

  workflowpipelinenextflowmetagenomicspacbioednamicrobiomeiontorrentilluminametabarcoding+ 10

  Nextflow

  •

  MIT License

  •152152 forks•243243 stars•1919 issues•11 pull request•Updated Apr 17, 2026Apr 17, 2026

• eager

  Public

  nf-core/eager’s past year of commit activity
  A fully reproducible and state-of-the-art ancient DNA analysis pipeline

  workflowbioinformaticspipeline+ 9

  workflowbioinformaticspipelinegenomenextflowmetagenomicspopulation-geneticsadnapathogen-genomicsnf-core+ 2

  Nextflow

  •

  MIT License

  •8989 forks•203203 stars•4949 issues•77 pull requests•Updated Apr 17, 2026Apr 17, 2026

• test-datasets

  Public
  Test data to be used for automated testing with the nf-core pipelines

  testingworkflownextflow+ 4

  testingworkflownextflowpipelinestest-datatest-datasetsnf-core

  MIT License

  •495495 forks•160160 stars•4040 issues•3030 pull requests•Updated Apr 17, 2026Apr 17, 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+ 5

  workflowbenchmarkpipelinenextflowvariant-callingstructural-variantsnf-coresmall-variants

  Nextflow

  •

  MIT License

  •2727 forks•4444 stars•2323 issues•22 pull requests•Updated Apr 17, 2026Apr 17, 2026

• setup-nextflow

  Public
  A GitHub action to install Nextflow

  nextflowactions

  nextflowactions

  TypeScript

  •

  MIT License

  •55 forks•2929 stars•44 issues•44 pull requests•Updated Apr 17, 2026Apr 17, 2026

• epitopeprediction

  Public

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

  workflowpipelinenextflow+ 4

  workflowpipelinenextflowepitope-predictionnf-coreepitopemhc-binding-prediction

  Nextflow

  •

  MIT License

  •3232 forks•5151 stars•2222 issues•33 pull requests•Updated Apr 17, 2026Apr 17, 2026

• createpanelrefs

  Public
  Generate Panel of Normals, models or other similar references from lots of samples

  workflowpipelinenextflow+ 1

  workflowpipelinenextflownf-core

  Nextflow

  •

  MIT License

  •1212 forks•1010 stars•77 issues•11 pull request•Updated Apr 17, 2026Apr 17, 2026

• proteinfold

  Public
  Protein 3D structure prediction pipeline

  workflowpipelinenextflow+ 8

  workflowpipelinenextflowprotein-structureprotein-sequencesprotein-foldingprotein-fold-predictionnf-corealphafold2colabfold+ 1

  HTML

  •

  MIT License

  •6767 forks•104104 stars•8585 issues•1414 pull requests•Updated Apr 17, 2026Apr 17, 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+ 7

  workflowquality-controlintegrationpipelinenextflowclusteringdimensionality-reductionsingle-cellnf-corescverse

  Nextflow

  •

  MIT License

  •6161 forks•9292 stars•3434 issues•22 pull requests•Updated Apr 16, 2026Apr 16, 2026

• rarevariantburden

  Public

  nf-core/rarevariantburden’s past year of commit activity
  Pipeline for performing consistent summary count based rare variant burden test, which is useful when we only have sequenced cases data. For example, we can com…

  workflowpipelinenextflow+ 5

  workflowpipelinenextflownf-coreburden-testrarevariantcocorvpublic-data-as-controlset

  Nextflow

  •

  MIT License

  •33 forks•00 stars•00 issues•33 pull requests•Updated Apr 16, 2026Apr 16, 2026

• bacass

  Public
  Simple bacterial assembly and annotation pipeline

  workflownanoporepipeline+ 9

  workflownanoporepipelinenextflowassemblydenovogenome-assemblydenovo-assemblybacterial-genomesnanopore-sequencing+ 2

  Nextflow

  •

  MIT License

  •6969 forks•8484 stars•2323 issues•66 pull requests•Updated Apr 16, 2026Apr 16, 2026

• sopa

  Public
  Nextflow version of Sopa - spatial omics pipeline and analysis

  workflowpipelinenextflow+ 6

  workflowpipelinenextflowsegmentationspatial-proteomicsnf-corespatial-transcriptomicsspatialdataspatial-omics

  Nextflow

  •

  MIT License

  •66 forks•1717 stars•22 issues•11 pull request•Updated Apr 16, 2026Apr 16, 2026

• callingcards

  Public
  A pipeline for processing calling cards data

  workflowpipelinenextflow+ 1

  workflowpipelinenextflownf-core

  Nextflow

  •

  MIT License

  •33 forks•55 stars•44 issues•33 pull requests•Updated Apr 15, 2026Apr 15, 2026

• rnavar

  Public

  nf-core/rnavar’s past year of commit activity
  gatk4 RNA variant calling pipeline

  workflowpipelinenextflow+ 6

  workflowpipelinenextflowrnaseqrnavariant-callingnf-coregatk4worflow

  Nextflow

  •

  MIT License

  •4646 forks•5959 stars•2020 issues•11 pull request•Updated Apr 15, 2026Apr 15, 2026