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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 392 951

  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 829

  4. sarek sarek Public

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

    Nextflow 528 499

  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
  • 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) 11 Updated Dec 30, 2025
  • 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 Dec 30, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 23 MIT 4 5 11 Updated Dec 30, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 83 MIT 253 112 20 Updated Dec 30, 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 392 MIT 951 392 (1 issue needs help) 165 Updated Dec 30, 2025
  • 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 528 MIT 499 312 (6 issues need help) 38 Updated Dec 30, 2025
  • lsmquant Public

    A pipeline for processing and analysis of light-sheet microscopy images.

    nf-core/lsmquant’s past year of commit activity
    Nextflow 5 MIT 1 0 4 Updated Dec 29, 2025
  • cageseq Public

    CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

    nf-core/cageseq’s past year of commit activity
    Nextflow 11 MIT 12 3 6 Updated Dec 24, 2025
  • epitopeprediction Public

    A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

    nf-core/epitopeprediction’s past year of commit activity
    Nextflow 49 MIT 28 14 4 Updated Dec 24, 2025
  • smrnaseq Public

    A small-RNA sequencing analysis pipeline

    nf-core/smrnaseq’s past year of commit activity
    Nextflow 98 MIT 131 12 (1 issue needs help) 1 Updated Dec 23, 2025
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