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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 290 224

  2. modules modules Public

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

    Nextflow 393 961

  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 842

  4. sarek sarek Public

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

    Nextflow 540 518

  5. configs configs Public

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

    Nextflow 107 339

  6. proposals proposals Public

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

    8 4

Repositories

Showing 10 of 181 repositories
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 85 MIT 259 115 31 Updated Feb 3, 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 1,192 MIT 842 31 15 Updated Feb 3, 2026
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 393 MIT 961 381 (1 issue needs help) 173 Updated Feb 3, 2026
  • ops Public

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

    nf-core/ops’s past year of commit activity
    Python 3 2 37 19 Updated Feb 3, 2026
  • mcmicro Public

    An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

    nf-core/mcmicro’s past year of commit activity
    Nextflow 30 MIT 20 34 6 Updated Feb 3, 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 5 Updated Feb 3, 2026
  • sopa Public

    Nextflow version of Sopa - spatial omics pipeline and analysis

    nf-core/sopa’s past year of commit activity
    Nextflow 13 MIT 3 1 2 Updated Feb 3, 2026
  • proteinannotator Public

    The best protein annotation pipeline in the world. Protein fasta → ??? → Annotations

    nf-core/proteinannotator’s past year of commit activity
    Nextflow 9 MIT 8 21 6 Updated Feb 3, 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 458 35 22 Updated Feb 3, 2026
  • epitopeprediction Public

    A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

    nf-core/epitopeprediction’s past year of commit activity
    Nextflow 51 MIT 30 15 1 Updated Feb 3, 2026
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