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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 283 222

  2. modules modules Public

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

    Nextflow 389 945

  3. rnaseq rnaseq Public

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

    Nextflow 1.2k 826

  4. sarek sarek Public

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

    Nextflow 505 492

  5. configs configs Public

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

    Nextflow 104 338

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 177 repositories
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 283 MIT 222 322 40 Updated Dec 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 389 MIT 945 392 (1 issue needs help) 165 Updated Dec 10, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 81 MIT 254 111 22 Updated Dec 10, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 22 MIT 4 5 8 Updated Dec 10, 2025
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 97 MIT 26 11 7 Updated Dec 10, 2025
  • nft-utils Public

    nf-test utility functions

    nf-core/nft-utils’s past year of commit activity
    Java 12 MIT 10 8 1 Updated Dec 9, 2025
  • ops Public

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

    nf-core/ops’s past year of commit activity
    Python 3 2 37 17 Updated Dec 9, 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
    144 MIT 449 35 16 Updated Dec 9, 2025
  • viralmetagenome Public

    A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.

    nf-core/viralmetagenome’s past year of commit activity
    Nextflow 26 MIT 5 10 0 Updated Dec 9, 2025
  • differentialabundance Public

    Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

    nf-core/differentialabundance’s past year of commit activity
    Nextflow 85 MIT 58 92 (1 issue needs help) 6 Updated Dec 9, 2025
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