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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 829

  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 4, 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 4 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
  • 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 5 Updated Jan 2, 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
    148 MIT 449 35 15 Updated Jan 2, 2026
  • viralmetagenome Public

    A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.

    nf-core/viralmetagenome’s past year of commit activity
    Nextflow 27 MIT 5 10 0 Updated Jan 2, 2026
  • 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 Jan 2, 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) 167 Updated Jan 1, 2026
  • 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 31, 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 529 MIT 498 312 (6 issues need help) 38 Updated Dec 30, 2025
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