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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 259 203

  2. modules modules Public

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

    Nextflow 355 862

  3. rnaseq rnaseq Public

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

    Nextflow 1k 763

  4. sarek sarek Public

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

    Nextflow 446 446

  5. configs configs Public

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

    Nextflow 99 310

  6. proposals proposals Public

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

    8 2

Repositories

Showing 10 of 163 repositories
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 73 MIT 19 26 3 Updated Jun 4, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 76 MIT 246 97 27 Updated Jun 4, 2025
  • proteinannotator Public

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

    nf-core/proteinannotator’s past year of commit activity
    Nextflow 4 MIT 5 25 9 Updated Jun 4, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 2 2 33 11 Updated Jun 4, 2025
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 355 MIT 862 418 (1 issue needs help) 176 Updated Jun 3, 2025
  • 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 1,035 MIT 763 61 11 Updated Jun 3, 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 65 MIT 29 33 (3 issues need help) 3 Updated Jun 3, 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
    129 MIT 407 33 12 Updated Jun 4, 2025
  • molkart Public

    A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

    nf-core/molkart’s past year of commit activity
    Nextflow 12 MIT 12 9 2 Updated Jun 4, 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 446 MIT 446 292 (6 issues need help) 40 Updated Jun 3, 2025
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