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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 322 255

  2. modules modules Public

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

    Nextflow 430 1.1k

  3. rnaseq rnaseq Public

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

    Nextflow 1.4k 897

  4. sarek sarek Public

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

    Nextflow 604 553

  5. configs configs Public

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

    Nextflow 112 374

  6. proposals proposals Public

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

    10 6

Repositories

Showing 10 of 201 repositories
  • taxmarker Public

    Identify taxonomically mislabelled sequences

    nf-core/taxmarker's past year of commit activity
    Nextflow 1 MIT 1 11 1 Updated Sep 25, 2026
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    nf-core/scdownstream's past year of commit activity
    Nextflow 115 MIT 66 24 (2 issues need help) 2 Updated Sep 25, 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 1,374 MIT 897 24 5 Updated Sep 26, 2026
  • spatialvi Public

    Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

    nf-core/spatialvi's past year of commit activity
    Nextflow 81 MIT 40 3 1 Updated Sep 25, 2026
  • actions Public

    Centralised GitHub Actions for nf-core.

    nf-core/actions's past year of commit activity
    TypeScript 0 MIT 1 0 4 Updated Sep 25, 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 430 MIT 1,100 303 (1 issue needs help) 171 Updated Sep 25, 2026
  • tumourevo Public

    Analysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)

    nf-core/tumourevo's past year of commit activity
    Nextflow 22 MIT 5 3 2 Updated Sep 26, 2026
  • scrnaseq Public

    Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

    nf-core/scrnaseq's past year of commit activity
    Nextflow 356 MIT 231 56 (1 issue needs help) 8 Updated Sep 25, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 98 MIT 298 122 20 Updated Sep 25, 2026
  • magmap Public

    Best-practice analysis pipeline for mapping reads to a (large) collections of genomes

    nf-core/magmap's past year of commit activity
    Nextflow 12 MIT 6 11 0 Updated Sep 25, 2026
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