Skip to content
@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.
README.md

Pinned Loading

  1. tools tools Public

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

    Python 260 204

  2. modules modules Public

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

    Nextflow 358 878

  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 773

  4. sarek sarek Public

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

    Nextflow 453 450

  5. configs configs Public

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

    Nextflow 100 314

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 165 repositories
  • drop Public

    Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

    nf-core/drop’s past year of commit activity
    Nextflow 5 MIT 2 3 3 Updated Jul 2, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 76 MIT 245 88 13 Updated Jul 2, 2025
  • configs Public

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

    nf-core/configs’s past year of commit activity
    Nextflow 100 MIT 314 8 11 Updated Jul 2, 2025
  • proteinfold Public

    Protein 3D structure prediction pipeline

    nf-core/proteinfold’s past year of commit activity
    Nextflow 82 MIT 58 42 (2 issues need help) 4 Updated Jul 2, 2025
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 159 MIT 112 33 (5 issues need help) 5 Updated Jul 2, 2025
  • drugresponseeval Public

    Pipeline for testing drug response prediction models in a statistically and biologically sound way.

    nf-core/drugresponseeval’s past year of commit activity
    Nextflow 20 MIT 4 7 2 Updated Jul 2, 2025
  • bacass Public

    Simple bacterial assembly and annotation pipeline

    nf-core/bacass’s past year of commit activity
    Nextflow 75 MIT 61 29 (1 issue needs help) 8 Updated Jul 2, 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 453 MIT 450 295 (6 issues need help) 41 Updated Jul 2, 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
    130 MIT 416 34 16 Updated Jul 2, 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 358 MIT 877 427 (1 issue needs help) 180 Updated Jul 2, 2025
View all repositories