Repositories list

• raredisease

  Public
  Call and score variants from WGS/WES of rare disease patients.

  workflowpipelinenextflow+ 9

  workflowpipelinenextflowdiagnosticsvariant-callingwgssnvwesvariant-annotationstructural-variants+ 2

  Nextflow

  •

  MIT License

  •6363 forks•116116 stars•5454 issues•66 pull requests•Updated Apr 26, 2026Apr 26, 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

  •864864 forks•1.3k1.3k stars•2222 issues•88 pull requests•Updated Apr 26, 2026Apr 26, 2026

• website

  Public
  Code and files for the main nf-core website.

  websitenextflownf-core

  websitenextflownf-core

  MDX

  •

  MIT License

  •289289 forks•9191 stars•115115 issues•3434 pull requests•Updated Apr 26, 2026Apr 26, 2026

• r-nf-core-utils

  Public

  nf-core/r-nf-core-utils’s past year of commit activity
  R nf-core utilities function

  rnextflownf-core+ 1

  rnextflownf-corenextflow-modules

  R

  •

  Other

  •11 fork•11 star•11 issue•00 pull requests•Updated Apr 26, 2026Apr 26, 2026

• modules

  Public
  Repository to host tool-specific module files for the Nextflow DSL2 community!

  modulesnextflowpipelines+ 4

  modulesnextflowpipelinesworkflowsnf-coredsl2nf-test

  Nextflow

  •

  MIT License

  •1k1k forks•413413 stars•293293 issues•189189 pull requests•Updated Apr 26, 2026Apr 26, 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

  •239239 forks•303303 stars•330330 issues•4747 pull requests•Updated Apr 26, 2026Apr 26, 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 26, 2026Apr 26, 2026

• configs

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

  bioinformaticsnextflowconfiguration+ 3

  bioinformaticsnextflowconfigurationpipelinesworkflowsnf-core

  Nextflow

  •

  MIT License

  •354354 forks•108108 stars•1212 issues•2929 pull requests•Updated Apr 25, 2026Apr 25, 2026

• createtaxdb

  Public

  nf-core/createtaxdb’s past year of commit activity
  Parallelised and automated construction of metagenomic classifier databases of different tools

  workflowdatabasepipeline+ 7

  workflowdatabasepipelinenextflowmetagenomicsprofilingnf-coredatabase-buildertaxonomic-profilingmetagenomic-profiling

  Nextflow

  •

  MIT License

  •1010 forks•2121 stars•1010 issues•22 pull requests•Updated Apr 25, 2026Apr 25, 2026

• cellpainting

  Public
  workflowpipelinenextflow+ 1

  workflowpipelinenextflownf-core

  Nextflow

  •

  MIT License

  •77 forks•88 stars•1414 issues•66 pull requests•Updated Apr 24, 2026Apr 24, 2026

• seqsubmit

  Public

  nf-core/seqsubmit’s past year of commit activity
  nf-core pipeline for data submission to ENA

  workflowpipelinenextflow+ 1

  workflowpipelinenextflownf-core

  Nextflow

  •

  MIT License

  •55 forks•55 stars•1717 issues•44 pull requests•Updated Apr 24, 2026Apr 24, 2026

• setup-nf-test

  Public
  Shell

  •

  MIT License

  •33 forks•77 stars•11 issue•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• riboseq

  Public
  Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.

  workflowpipelinenextflow+ 1

  workflowpipelinenextflownf-core

  Nextflow

  •

  MIT License

  •1818 forks•2525 stars•1616 issues•33 pull requests•Updated Apr 24, 2026Apr 24, 2026

• funcscan

  Public
  (Meta-)genome screening for functional and natural product gene sequences

  workflowbioinformaticspipeline+ 17

  workflowbioinformaticspipelinenextflowampassemblyfunctionmetagenomicsamrscreening+ 10

  Nextflow

  •

  MIT License

  •3535 forks•105105 stars•1919 issues•33 pull requests•Updated Apr 24, 2026Apr 24, 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 24, 2026Apr 24, 2026

• rnavar

  Public
  gatk4 RNA variant calling pipeline

  workflowpipelinenextflow+ 6

  workflowpipelinenextflowrnaseqrnavariant-callingnf-coregatk4worflow

  Nextflow

  •

  MIT License

  •4646 forks•6060 stars•2121 issues•11 pull request•Updated Apr 24, 2026Apr 24, 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 24, 2026Apr 24, 2026

• eager

  Public
  A fully reproducible and state-of-the-art ancient DNA analysis pipeline

  workflowbioinformaticspipeline+ 9

  workflowbioinformaticspipelinegenomenextflowmetagenomicspopulation-geneticsadnapathogen-genomicsnf-core+ 2

  Nextflow

  •

  MIT License

  •8888 forks•203203 stars•4949 issues•55 pull requests•Updated Apr 24, 2026Apr 24, 2026

• genomeqc

  Public
  Compare the quality of multiple genomes, along with their annotations.

  bioinformaticsquality-controlpipeline+ 5

  bioinformaticsquality-controlpipelinegenomicsnextflowphylogenetic-treesgenome-assembly-evaluationnf-core

  Nextflow

  •

  MIT License

  •2323 forks•2020 stars•7070 issues•44 pull requests•Updated Apr 24, 2026Apr 24, 2026

• pixelator

  Public

  nf-core/pixelator’s past year of commit activity
  Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

  workflowpipelinenextflow+ 7

  workflowpipelinenextflowproteinspixelatorsingle-cellnf-coresingle-cell-omicsmolecular-pixelationpixelgen-technologies

  Nextflow

  •

  MIT License

  •99 forks•1313 stars•22 issues•22 pull requests•Updated Apr 24, 2026Apr 24, 2026

• fetchngs

  Public
  Pipeline to fetch metadata and raw FastQ files from public databases

  workflowpipelinenextflow+ 8

  workflowpipelinenextflowdownloadgeofastqsynapsesraenanf-core+ 1

  Nextflow

  •

  MIT License

  •9090 forks•189189 stars•3636 issues•1212 pull requests•Updated Apr 24, 2026Apr 24, 2026

• diseasemodulediscovery

  Public
  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 24, 2026Apr 24, 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+ 6

  pipelinenextflowimage-processingstitchingsegmentationimage-analysisnf-corelight-sheet-microcopy3dunet

  Nextflow

  •

  MIT License

  •33 forks•66 stars•11 issue•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• proteinfold

  Public

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

  workflowpipelinenextflow+ 8

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

  HTML

  •

  MIT License

  •6868 forks•104104 stars•8888 issues•1414 pull requests•Updated Apr 24, 2026Apr 24, 2026

• oncoanalyser

  Public
  A comprehensive cancer DNA/RNA analysis and reporting pipeline

  workflowpipelinenextflow+ 14

  workflowpipelinenextflowcancerpanelngsclinicaldnarnawgs+ 7

  Nextflow

  •

  MIT License

  •2828 forks•107107 stars•1414 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• setup-nextflow

  Public
  A GitHub action to install Nextflow

  nextflowactions

  nextflowactions

  TypeScript

  •

  MIT License

  •55 forks•2929 stars•44 issues•66 pull requests•Updated Apr 24, 2026Apr 24, 2026

• funcprofiler

  Public
  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 23, 2026Apr 23, 2026

• airrflow

  Public
  B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

  workflowpipelinenextflow+ 6

  workflowpipelinenextflownf-coreb-cellrepseqimmcantationimmunorepertoireairr

  Nextflow

  •

  MIT License

  •5252 forks•7575 stars•3535 issues•33 pull requests•Updated Apr 23, 2026Apr 23, 2026

• hadge

  Public

  nf-core/hadge’s past year of commit activity
  Comprehensive pipeline for donor demultiplexing in single cell

  workflowpipelinenextflow+ 12

  workflowpipelinenextflowsingle-celldeconvolutiondemultiplexingnf-coredonor-deconvolutioncell-hashinghto+ 5

  Nextflow

  •

  MIT License

  •88 forks•2525 stars•1212 issues•22 pull requests•Updated Apr 23, 2026Apr 23, 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

  •497497 forks•160160 stars•4040 issues•3030 pull requests•Updated Apr 23, 2026Apr 23, 2026