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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 285 223

  2. modules modules Public

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

    Nextflow 392 950

  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 830

  4. sarek sarek Public

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

    Nextflow 529 498

  5. configs configs Public

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

    Nextflow 106 339

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 177 repositories
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 83 MIT 253 113 20 Updated Jan 5, 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 1,177 MIT 830 35 13 Updated Jan 5, 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 392 MIT 950 385 (1 issue needs help) 163 Updated Jan 5, 2026
  • scrnaseq Public

    Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

    nf-core/scrnaseq’s past year of commit activity
    Nextflow 309 MIT 206 74 (1 issue needs help) 8 Updated Jan 5, 2026
  • nf-core-utils Public

    Nextflow plugin for nf-core utils

    nf-core/nf-core-utils’s past year of commit activity
    Groovy 1 Apache-2.0 0 10 2 Updated Jan 5, 2026
  • riboseq Public

    Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.

    nf-core/riboseq’s past year of commit activity
    Nextflow 20 MIT 17 13 5 Updated Jan 5, 2026
  • createtaxdb Public

    Parallelised and automated construction of metagenomic classifier databases of different tools

    nf-core/createtaxdb’s past year of commit activity
    Nextflow 20 MIT 10 8 0 Updated Jan 5, 2026
  • mhcquant Public

    Identify and quantify MHC eluted peptides from mass spectrometry raw data

    nf-core/mhcquant’s past year of commit activity
    Nextflow 42 MIT 30 14 (1 issue needs help) 3 Updated Jan 5, 2026
  • nanostring Public

    An analysis pipeline for Nanostring nCounter expression data.

    nf-core/nanostring’s past year of commit activity
    Nextflow 16 MIT 11 7 3 Updated Jan 2, 2026
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    nf-core/scdownstream’s past year of commit activity
    Nextflow 81 MIT 47 35 (3 issues need help) 7 Updated Jan 2, 2026
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