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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 292 224

  2. modules modules Public

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

    Nextflow 398 967

  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 847

  4. sarek sarek Public

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

    Nextflow 546 522

  5. configs configs Public

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

    Nextflow 107 340

  6. proposals proposals Public

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

    8 4

Repositories

Showing 10 of 182 repositories
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 292 MIT 224 331 41 Updated Feb 17, 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 398 MIT 967 380 (1 issue needs help) 169 Updated Feb 17, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 85 MIT 267 115 35 Updated Feb 17, 2026
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 114 MIT 57 49 3 Updated Feb 17, 2026
  • mhcquant Public

    Identify and quantify MHC eluted peptides from mass spectrometry raw data

    nf-core/mhcquant’s past year of commit activity
    Nextflow 44 MIT 33 14 (1 issue needs help) 2 Updated Feb 17, 2026
  • hadge Public

    Comprehensive pipeline for donor demultiplexing in single cell

    nf-core/hadge’s past year of commit activity
    Nextflow 25 MIT 8 12 3 Updated Feb 17, 2026
  • methylarray Public

    Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.

    nf-core/methylarray’s past year of commit activity
    Nextflow 6 MIT 4 8 0 Updated Feb 17, 2026
  • coproid Public

    Coprolite host Identification pipeline

    nf-core/coproid’s past year of commit activity
    Nextflow 12 MIT 4 1 0 Updated Feb 17, 2026
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 26 MIT 4 6 4 Updated Feb 17, 2026
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 102 MIT 27 11 6 Updated Feb 17, 2026
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