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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 325 264

  2. modules modules Public

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

    Nextflow 431 1.1k

  3. rnaseq rnaseq Public

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

    Nextflow 1.4k 905

  4. sarek sarek Public

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

    Nextflow 614 561

  5. configs configs Public

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

    Nextflow 113 375

  6. proposals proposals Public

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

    10 6

Repositories

Showing 10 of 201 repositories
  • 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 113 MIT 375 14 34 Updated Oct 13, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 98 MIT 299 122 23 Updated Oct 13, 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 614 MIT 561 264 (5 issues need help) 45 Updated Oct 13, 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 7 MIT 4 0 0 Updated Oct 12, 2026
  • pacvar Public

    Longread PacBio sequencing processing for WGS and PureTarget

    nf-core/pacvar's past year of commit activity
    Nextflow 16 MIT 14 9 (1 issue needs help) 1 Updated Oct 12, 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 117 MIT 68 11 1 Updated Oct 12, 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
    163 MIT 536 43 33 Updated Oct 12, 2026
  • pathogenepidemiology Public

    [DEVELOPMENT UNDERWAY] A profile-based pipeline for genomic epidemiological analysis of predefined pathogens.

    nf-core/pathogenepidemiology's past year of commit activity
    Nextflow 3 MIT 2 12 (2 issues need help) 1 Updated Oct 12, 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 431 MIT 1,112 289 (1 issue needs help) 184 Updated Oct 12, 2026
  • 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 30 MIT 11 6 0 Updated Oct 12, 2026
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