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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 293 224

  2. modules modules Public

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

    Nextflow 402 970

  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 848

  4. sarek sarek Public

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

    Nextflow 553 526

  5. configs configs Public

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

    Nextflow 107 341

  6. proposals proposals Public

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

    8 4

Repositories

Showing 10 of 183 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 402 MIT 970 477 (1 issue needs help) 149 Updated Feb 26, 2026
  • hlatyping Public

    Precision HLA typing from next-generation sequencing data

    nf-core/hlatyping’s past year of commit activity
    Nextflow 78 MIT 34 11 3 Updated Feb 26, 2026
  • rnaseq Public

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

    nf-core/rnaseq’s past year of commit activity
    Nextflow 1,210 MIT 848 28 16 Updated Feb 26, 2026
  • cageseq Public

    CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

    nf-core/cageseq’s past year of commit activity
    Nextflow 11 MIT 12 3 8 Updated Feb 26, 2026
  • configs Public

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

    nf-core/configs’s past year of commit activity
    Nextflow 107 MIT 341 11 (1 issue needs help) 30 Updated Feb 26, 2026
  • 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
    150 MIT 462 36 20 Updated Feb 26, 2026
  • 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 22 MIT 38 24 (2 issues need help) 9 Updated Feb 26, 2026
  • 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 9 2 1 Updated Feb 26, 2026
  • phaseimpute Public

    A bioinformatics pipeline to phase and impute genetic data

    nf-core/phaseimpute’s past year of commit activity
    Nextflow 28 MIT 20 19 3 Updated Feb 26, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 85 MIT 271 115 37 Updated Feb 26, 2026
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