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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 283 223

  2. modules modules Public

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

    Nextflow 389 946

  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 828

  4. sarek sarek Public

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

    Nextflow 527 495

  5. configs configs Public

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

    Nextflow 104 339

  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
  • 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 946 389 (1 issue needs help) 160 Updated Dec 15, 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
    145 MIT 450 35 15 Updated Dec 15, 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 527 MIT 495 308 (6 issues need help) 37 Updated Dec 15, 2025
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 112 MIT 55 46 5 Updated Dec 15, 2025
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    nf-core/demultiplex’s past year of commit activity
    Nextflow 51 MIT 46 24 0 Updated Dec 15, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 81 MIT 253 112 20 Updated Dec 15, 2025
  • seqinspector Public

    Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.

    nf-core/seqinspector’s past year of commit activity
    Nextflow 15 MIT 37 30 (2 issues need help) 8 Updated Dec 15, 2025
  • pixelator Public

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

    nf-core/pixelator’s past year of commit activity
    Nextflow 13 MIT 8 2 0 Updated Dec 15, 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 16 Updated Dec 15, 2025
  • methylong Public

    Extract methylation calls from long reads (ONT/ PacBio)

    nf-core/methylong’s past year of commit activity
    Nextflow 19 MIT 5 2 1 Updated Dec 15, 2025
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