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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 260 204

  2. modules modules Public

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

    Nextflow 356 875

  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 771

  4. sarek sarek Public

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

    Nextflow 453 449

  5. configs configs Public

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

    Nextflow 100 313

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 164 repositories
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 19 MIT 6 5 7 Updated Jun 28, 2025
  • demo Public

    nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.

    nf-core/demo’s past year of commit activity
    Nextflow 6 MIT 12 6 0 Updated Jun 27, 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 356 MIT 875 426 (1 issue needs help) 172 Updated Jun 27, 2025
  • pathogensurveillance Public

    Surveillance of pathogens using population genomics and sequencing

    nf-core/pathogensurveillance’s past year of commit activity
    Nextflow 30 MIT 7 58 (3 issues need help) 1 Updated Jun 27, 2025
  • phaseimpute Public

    A bioinformatics pipeline to phase and impute genetic data

    nf-core/phaseimpute’s past year of commit activity
    Nextflow 22 MIT 20 12 0 Updated Jun 27, 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 11 Updated Jun 27, 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 Jun 27, 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 313 8 9 Updated Jun 27, 2025
  • funcscan Public

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

    nf-core/funcscan’s past year of commit activity
    Nextflow 88 MIT 27 18 3 Updated Jun 27, 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 Jun 27, 2025
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