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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 327 265

  2. modules modules Public

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

    Nextflow 432 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 904

  4. sarek sarek Public

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

    Nextflow 614 561

  5. configs configs Public

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

    Nextflow 114 375

  6. proposals proposals Public

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

    10 6

Repositories

Showing 10 of 202 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 432 MIT 1,120 291 (1 issue needs help) 185 Updated Oct 15, 2026
  • msproteomics Public
    nf-core/msproteomics's past year of commit activity
    Nextflow 0 MIT 1 0 2 Updated Oct 15, 2026
  • magmap Public

    Best-practice analysis pipeline for mapping reads to a (large) collections of genomes

    nf-core/magmap's past year of commit activity
    Nextflow 13 MIT 6 15 1 Updated Oct 15, 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 561 262 (5 issues need help) 50 Updated Oct 15, 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 265 368 92 Updated Oct 15, 2026
  • isoseq Public

    Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

    nf-core/isoseq's past year of commit activity
    Nextflow 57 MIT 22 7 1 Updated Oct 15, 2026
  • rnasplice Public

    rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

    nf-core/rnasplice's past year of commit activity
    Nextflow 69 MIT 43 5 2 Updated Oct 15, 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 538 43 35 Updated Oct 15, 2026
  • spatialaxe Public

    A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data

    nf-core/spatialaxe's past year of commit activity
    Python 46 MIT 25 49 8 Updated Oct 15, 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 15, 2026
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