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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 266 208

  2. modules modules Public

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

    Nextflow 370 896

  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 794

  4. sarek sarek Public

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

    Nextflow 472 472

  5. configs configs Public

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

    Nextflow 103 324

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 169 repositories
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 370 MIT 896 380 (1 issue needs help) 171 Updated Sep 4, 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 Sep 4, 2025
  • taxprofiler Public

    Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

    nf-core/taxprofiler’s past year of commit activity
    Nextflow 161 MIT 56 42 (1 issue needs help) 6 Updated Sep 4, 2025
  • abotyper Public

    A pipeline for characterising the Human Blood Group and Red Cell Antigens using Oxford Nanopore third-generation sequencing data.

    nf-core/abotyper’s past year of commit activity
    Nextflow 0 MIT 1 0 1 Updated Sep 4, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 77 MIT 246 92 16 Updated Sep 4, 2025
  • methylseq Public

    Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

    nf-core/methylseq’s past year of commit activity
    Nextflow 172 MIT 159 20 (1 issue needs help) 4 Updated Sep 4, 2025
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 85 MIT 24 9 2 Updated Sep 4, 2025
  • chipseq Public

    ChIP-seq peak-calling, QC and differential analysis pipeline.

    nf-core/chipseq’s past year of commit activity
    Nextflow 219 MIT 158 29 (1 issue needs help) 6 Updated Sep 3, 2025
  • nft-utils Public

    nf-test utility functions

    nf-core/nft-utils’s past year of commit activity
    Java 11 MIT 11 6 1 Updated Sep 3, 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
    138 MIT 434 35 16 Updated Sep 3, 2025
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