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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 908

  4. sarek sarek Public

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

    Nextflow 614 564

  5. configs configs Public

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

    Nextflow 114 377

  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
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 99 MIT 301 125 35 Updated Oct 22, 2026
  • abotyper Public

    A pipeline for characterising the Human Blood Group and Red Cell Antigens using Oxford Nanopore third-generation sequencing data.

    nf-core/abotyper's past year of commit activity
    Python 4 MIT 2 0 7 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 564 262 (5 issues need help) 50 Updated Oct 22, 2026
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow's past year of commit activity
    TypeScript 31 MIT 5 4 15 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 93 Updated Oct 22, 2026
  • strict-syntax-health Public

    Track Nextflow strict syntax linting health across nf-core pipelines

    nf-core/strict-syntax-health's past year of commit activity
    Python 7 MIT 4 0 0 Updated Oct 22, 2026
  • plasmodiumdrugres Public

    Pipeline for analyzing drug resistance markers from Plasmodium microhaplotype data. Translates variants into amino acid changes at drug resistance loci and estimates allele frequencies and prevalences at both single-locus and multi-locus levels. Microhaplotype data can be supplied in the form of an allele table or a PMO file.

    nf-core/plasmodiumdrugres's past year of commit activity
    Nextflow 2 MIT 2 14 0 Updated Oct 21, 2026
  • pathogenepidemiology Public

    [DEVELOPMENT UNDERWAY] A profile-based pipeline for genomic epidemiological analysis of predefined pathogens.

    nf-core/pathogenepidemiology's past year of commit activity
    Nextflow 3 MIT 2 20 (2 issues need help) 1 Updated Oct 21, 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 1,125 286 (1 issue needs help) 190 Updated Oct 21, 2026
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    nf-core/demultiplex's past year of commit activity
    Nextflow 61 MIT 57 19 (1 issue needs help) 2 Updated Oct 21, 2026
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