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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 260 203

  2. modules modules Public

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

    Nextflow 356 869

  3. rnaseq rnaseq Public

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

    Nextflow 1k 768

  4. sarek sarek Public

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

    Nextflow 451 447

  5. configs configs Public

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

    Nextflow 99 311

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 163 repositories
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 74 MIT 20 23 3 Updated Jun 16, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 76 MIT 246 91 18 Updated Jun 16, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 2 2 33 12 Updated Jun 16, 2025
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 356 MIT 869 415 (1 issue needs help) 172 Updated Jun 15, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 19 MIT 6 5 6 Updated Jun 15, 2025
  • createtaxdb Public

    Parallelised and automated construction of metagenomic classifier databases of different tools

    nf-core/createtaxdb’s past year of commit activity
    Nextflow 9 MIT 7 7 2 Updated Jun 15, 2025
  • 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 16 MIT 20 28 6 Updated Jun 15, 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
    130 MIT 413 34 16 Updated Jun 15, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 260 MIT 203 270 39 Updated Jun 15, 2025
  • fastquorum Public

    Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

    nf-core/fastquorum’s past year of commit activity
    Nextflow 23 MIT 13 10 (1 issue needs help) 1 Updated Jun 13, 2025
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