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@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.
README.md

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  1. tools tools Public

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

    Python 327 266

  2. modules modules Public

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

    Nextflow 433 1.1k

  3. rnaseq rnaseq Public

    RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

    Nextflow 1.4k 909

  4. sarek sarek Public

    Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

    Nextflow 614 563

  5. configs configs Public

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

    Nextflow 114 376

  6. proposals proposals Public

    Where new ideas for nf-core pipelines, special interest groups and more are proposed

    10 6

Repositories

Showing 10 of 203 repositories
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    nf-core/demultiplex's past year of commit activity
    Nextflow 61 MIT 57 18 (1 issue needs help) 1 Updated Oct 22, 2026
  • modules Public

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

    nf-core/modules's past year of commit activity
    Nextflow 433 MIT 1,126 288 (1 issue needs help) 190 Updated Oct 22, 2026
  • tools Public

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

    nf-core/tools's past year of commit activity
    Python 327 MIT 266 370 97 Updated Oct 22, 2026
  • drugresponseeval Public

    Pipeline for testing drug response prediction models in a statistically and biologically sound way.

    nf-core/drugresponseeval's past year of commit activity
    Nextflow 30 MIT 11 5 0 Updated Oct 22, 2026
  • sarek Public

    Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

    nf-core/sarek's past year of commit activity
    Nextflow 614 MIT 563 260 (5 issues need help) 52 Updated Oct 22, 2026
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    nf-core/scdownstream's past year of commit activity
    Nextflow 117 MIT 68 12 4 Updated Oct 22, 2026
  • test-datasets Public

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

    nf-core/test-datasets's past year of commit activity
    163 MIT 541 43 34 Updated Oct 22, 2026
  • diseasemodulediscovery Public

    A pipeline for network-based disease module identification.

    nf-core/diseasemodulediscovery's past year of commit activity
    Nextflow 6 MIT 6 38 12 Updated Oct 22, 2026
  • mhcquant Public

    Identify and quantify MHC eluted peptides from mass spectrometry raw data

    nf-core/mhcquant's past year of commit activity
    Nextflow 50 MIT 36 9 3 Updated Oct 22, 2026
  • raredisease Public

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

    nf-core/raredisease's past year of commit activity
    Nextflow 126 MIT 71 12 5 Updated Oct 22, 2026
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