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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 261 206

  2. modules modules Public

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

    Nextflow 360 879

  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 456 451

  5. configs configs Public

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

    Nextflow 101 315

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 166 repositories
  • cellpainting Public
    nf-core/cellpainting’s past year of commit activity
    Nextflow 5 MIT 5 14 3 Updated Jul 7, 2025
  • raredisease Public

    Call and score variants from WGS/WES of rare disease patients.

    nf-core/raredisease’s past year of commit activity
    Nextflow 103 MIT 46 39 3 Updated Jul 7, 2025
  • nf-core-utils Public

    Nextflow plugin for nf-core utils

    nf-core/nf-core-utils’s past year of commit activity
    Groovy 1 Apache-2.0 0 6 2 Updated Jul 7, 2025
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 1 2 16 4 Updated Jul 7, 2025
  • logos Public

    Host nf-core logos and templates for making new logos

    nf-core/logos’s past year of commit activity
    6 MIT 13 0 1 Updated Jul 7, 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 Jul 7, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 261 MIT 206 274 30 Updated Jul 7, 2025
  • 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 7, 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 101 MIT 315 8 9 Updated Jul 7, 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
    131 MIT 417 34 17 Updated Jul 7, 2025
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