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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 277 218

  2. modules modules Public

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

    Nextflow 384 930

  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 807

  4. sarek sarek Public

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

    Nextflow 499 488

  5. configs configs Public

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

    Nextflow 104 333

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 172 repositories
  • pixelator Public

    Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

    nf-core/pixelator’s past year of commit activity
    Nextflow 12 MIT 8 1 1 Updated Nov 5, 2025
  • sopa Public

    Nextflow version of Sopa - spatial omics pipeline and analysis

    nf-core/sopa’s past year of commit activity
    Nextflow 11 MIT 1 1 2 Updated Nov 5, 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 168 MIT 59 43 (1 issue needs help) 6 Updated Nov 5, 2025
  • rnavar Public

    gatk4 RNA variant calling pipeline

    nf-core/rnavar’s past year of commit activity
    Nextflow 55 MIT 41 18 1 Updated Nov 5, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 81 MIT 253 109 24 Updated Nov 5, 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
    142 MIT 445 35 16 Updated Nov 5, 2025
  • methylong Public

    Extract methylation calls from long reads (ONT/ PacBio)

    nf-core/methylong’s past year of commit activity
    Nextflow 16 MIT 3 2 1 Updated Nov 5, 2025
  • createpanelrefs Public

    Generate Panel of Normals, models or other similar references from lots of samples

    nf-core/createpanelrefs’s past year of commit activity
    Nextflow 11 MIT 10 6 2 Updated Nov 5, 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 384 MIT 930 395 (1 issue needs help) 161 Updated Nov 5, 2025
  • ribomsqc Public

    QC pipeline that monitors mass spectrometer performance in ribonucleoside analysis

    nf-core/ribomsqc’s past year of commit activity
    R 0 MIT 2 0 1 Updated Nov 5, 2025
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