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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 290 224

  2. modules modules Public

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

    Nextflow 394 963

  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 842

  4. sarek sarek Public

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

    Nextflow 541 517

  5. configs configs Public

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

    Nextflow 107 339

  6. proposals proposals Public

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

    8 4

Repositories

Showing 10 of 181 repositories
  • 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 57 49 4 Updated Feb 4, 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 394 MIT 963 378 (1 issue needs help) 165 Updated Feb 4, 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 541 MIT 517 303 (5 issues need help) 40 Updated Feb 4, 2026
  • rnaseq Public

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

    nf-core/rnaseq’s past year of commit activity
    Nextflow 1,192 MIT 842 31 16 Updated Feb 4, 2026
  • mcmicro Public

    An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

    nf-core/mcmicro’s past year of commit activity
    Nextflow 30 MIT 20 36 6 Updated Feb 4, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 85 MIT 260 115 31 Updated Feb 4, 2026
  • cellpainting Public
    nf-core/cellpainting’s past year of commit activity
    Nextflow 7 MIT 6 14 4 Updated Feb 4, 2026
  • ops Public

    Different *Ops related scripts for the nf-core org.

    nf-core/ops’s past year of commit activity
    Python 3 2 37 19 Updated Feb 4, 2026
  • crisprseq Public

    A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).

    nf-core/crisprseq’s past year of commit activity
    Nextflow 52 MIT 31 25 4 Updated Feb 4, 2026
  • sopa Public

    Nextflow version of Sopa - spatial omics pipeline and analysis

    nf-core/sopa’s past year of commit activity
    Nextflow 13 MIT 3 1 2 Updated Feb 4, 2026
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