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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 284 223

  2. modules modules Public

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

    Nextflow 389 950

  3. rnaseq rnaseq Public

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

    Nextflow 1.2k 829

  4. sarek sarek Public

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

    Nextflow 529 498

  5. configs configs Public

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

    Nextflow 105 339

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 177 repositories
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 389 MIT 950 392 (1 issue needs help) 168 Updated Dec 22, 2025
  • sopa Public

    Nextflow version of Sopa - spatial omics pipeline and analysis

    nf-core/sopa’s past year of commit activity
    Nextflow 11 MIT 1 1 3 Updated Dec 22, 2025
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 112 MIT 55 47 4 Updated Dec 22, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 83 MIT 253 112 20 Updated Dec 22, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 22 MIT 4 5 11 Updated Dec 22, 2025
  • cageseq Public

    CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

    nf-core/cageseq’s past year of commit activity
    Nextflow 11 MIT 12 3 5 Updated Dec 21, 2025
  • funcscan Public

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

    nf-core/funcscan’s past year of commit activity
    Nextflow 97 MIT 33 23 1 Updated Dec 21, 2025
  • 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
    146 MIT 450 35 15 Updated Dec 21, 2025
  • diseasemodulediscovery Public

    A pipeline for network-based disease module identification.

    nf-core/diseasemodulediscovery’s past year of commit activity
    Python 5 MIT 3 35 5 Updated Dec 19, 2025
  • riboseq Public

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

    nf-core/riboseq’s past year of commit activity
    Nextflow 18 MIT 15 13 6 Updated Dec 19, 2025
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