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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 271 212

  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 799

  4. sarek sarek Public

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

    Nextflow 486 477

  5. configs configs Public

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

    Nextflow 103 329

  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
  • ops Public

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

    nf-core/ops’s past year of commit activity
    Python 3 2 34 14 Updated Oct 4, 2025
  • funcscan Public

    (Meta-)genome screening for functional and natural product gene sequences

    nf-core/funcscan’s past year of commit activity
    Nextflow 91 MIT 33 23 2 Updated Oct 4, 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 378 MIT 908 380 (1 issue needs help) 167 Updated Oct 4, 2025
  • 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
    140 MIT 439 34 17 Updated Oct 4, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 78 MIT 248 99 19 Updated Oct 4, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 21 MIT 5 5 7 Updated Oct 3, 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 3, 2025
  • proteinfamilies Public

    Generation and update of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 20 MIT 3 7 0 Updated Oct 3, 2025
  • longraredisease Public

    Long read sequencing pipeline to identify variants in patients with neurodevelopmental disorders

    nf-core/longraredisease’s past year of commit activity
    Nextflow 3 MIT 2 1 2 Updated Oct 3, 2025
  • 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 164 MIT 57 45 (1 issue needs help) 4 Updated Oct 3, 2025
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