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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 287 224

  2. modules modules Public

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

    Nextflow 393 958

  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 841

  4. sarek sarek Public

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

    Nextflow 538 518

  5. configs configs Public

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

    Nextflow 107 340

  6. proposals proposals Public

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

    8 4

Repositories

Showing 10 of 181 repositories
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 393 MIT 958 381 (1 issue needs help) 175 Updated Jan 29, 2026
  • mhcquant Public

    Identify and quantify MHC eluted peptides from mass spectrometry raw data

    nf-core/mhcquant’s past year of commit activity
    Nextflow 43 MIT 32 13 (1 issue needs help) 2 Updated Jan 29, 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 83 MIT 51 38 (3 issues need help) 2 Updated Jan 29, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 84 MIT 254 115 26 Updated Jan 29, 2026
  • metapep Public

    From metagenomes to epitopes and beyond

    nf-core/metapep’s past year of commit activity
    Nextflow 12 MIT 8 16 2 Updated Jan 29, 2026
  • 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 538 MIT 518 304 (5 issues need help) 39 Updated Jan 29, 2026
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 287 MIT 224 328 46 Updated Jan 29, 2026
  • taxprofiler Public

    Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

    nf-core/taxprofiler’s past year of commit activity
    Nextflow 176 MIT 59 46 (1 issue needs help) 6 Updated Jan 29, 2026
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 100 MIT 27 10 6 Updated Jan 29, 2026
  • strict-syntax-health Public

    Track Nextflow strict syntax linting health across nf-core pipelines

    nf-core/strict-syntax-health’s past year of commit activity
    Python 5 MIT 1 0 0 Updated Jan 29, 2026
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