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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 776

  4. sarek sarek Public

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

    Nextflow 457 452

  5. configs configs Public

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

    Nextflow 101 316

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 168 repositories
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 104 MIT 46 39 2 Updated Jul 10, 2025
  • ops Public

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

    nf-core/ops’s past year of commit activity
    Python 3 2 33 10 Updated Jul 10, 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 457 MIT 452 293 (6 issues need help) 39 Updated Jul 10, 2025
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 160 MIT 112 37 (4 issues need help) 5 Updated Jul 10, 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 360 MIT 879 429 (1 issue needs help) 180 Updated Jul 10, 2025
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    nf-core/demultiplex’s past year of commit activity
    Nextflow 47 MIT 44 22 2 Updated Jul 10, 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 10, 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 4 2 Updated Jul 10, 2025
  • genomeqc Public

    Compare the quality of multiple genomes, along with their annotations.

    nf-core/genomeqc’s past year of commit activity
    Nextflow 14 MIT 16 50 (2 issues need help) 6 Updated Jul 10, 2025
  • nft-utils Public

    nf-test utility functions

    nf-core/nft-utils’s past year of commit activity
    Java 11 MIT 11 6 0 Updated Jul 10, 2025
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