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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 272 212

  2. modules modules Public

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

    Nextflow 378 908

  3. rnaseq rnaseq Public

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

    Nextflow 1.1k 798

  4. sarek sarek Public

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

    Nextflow 487 478

  5. configs configs Public

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

    Nextflow 104 329

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 171 repositories
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 87 MIT 27 11 2 Updated Oct 7, 2025
  • rarevariantburden Public

    Pipeline for performing consistent summary count based rare variant burden test, which is useful when we only have sequenced cases data. For example, we can compare the cases against public summary count data, such as gnomAD.

    nf-core/rarevariantburden’s past year of commit activity
    Nextflow 0 MIT 2 0 2 Updated Oct 7, 2025
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 1 2 27 4 Updated Oct 7, 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 24 MIT 20 31 5 Updated Oct 7, 2025
  • epitopeprediction Public

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

    nf-core/epitopeprediction’s past year of commit activity
    Nextflow 47 MIT 29 11 2 Updated Oct 7, 2025
  • mhcquant Public

    Identify and quantify MHC eluted peptides from mass spectrometry raw data

    nf-core/mhcquant’s past year of commit activity
    Nextflow 38 MIT 30 5 (1 issue needs help) 4 Updated Oct 7, 2025
  • ops Public

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

    nf-core/ops’s past year of commit activity
    Python 3 2 37 14 Updated Oct 7, 2025
  • logos Public

    Host nf-core logos and templates for making new logos

    nf-core/logos’s past year of commit activity
    7 MIT 14 0 1 Updated Oct 7, 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 487 MIT 478 298 (6 issues need help) 39 Updated Oct 7, 2025
  • proteinfamilies Public

    Generation and update of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 20 MIT 3 7 2 Updated Oct 7, 2025
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