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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 265 208

  2. modules modules Public

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

    Nextflow 367 894

  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 791

  4. sarek sarek Public

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

    Nextflow 470 467

  5. configs configs Public

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

    Nextflow 103 324

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 169 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 367 MIT 894 376 (1 issue needs help) 168 Updated Sep 2, 2025
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 81 MIT 24 18 2 Updated Sep 2, 2025
  • circrna Public

    circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

    nf-core/circrna’s past year of commit activity
    Nextflow 57 MIT 32 11 2 Updated Sep 2, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 77 MIT 246 92 19 Updated Sep 2, 2025
  • 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 70 MIT 38 36 (3 issues need help) 6 Updated Sep 1, 2025
  • nf-core-utils Public

    Nextflow plugin for nf-core utils

    nf-core/nf-core-utils’s past year of commit activity
    Groovy 1 Apache-2.0 0 6 1 Updated Sep 1, 2025
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 162 MIT 117 16 (1 issue needs help) 7 Updated Sep 1, 2025
  • bacass Public

    Simple bacterial assembly and annotation pipeline

    nf-core/bacass’s past year of commit activity
    Nextflow 75 MIT 62 22 (1 issue needs help) 3 Updated Sep 1, 2025
  • pixelator Public

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

    nf-core/pixelator’s past year of commit activity
    Nextflow 11 MIT 7 1 2 Updated Sep 1, 2025
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    nf-core/demultiplex’s past year of commit activity
    Nextflow 50 MIT 44 23 2 Updated Sep 1, 2025
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