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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 295 230

  2. modules modules Public

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

    Nextflow 403 1k

  3. rnaseq rnaseq Public

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

    Nextflow 1.2k 855

  4. sarek sarek Public

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

    Nextflow 554 525

  5. configs configs Public

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

    Nextflow 108 348

  6. proposals proposals Public

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

    8 4

Repositories

Showing 10 of 184 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 403 MIT 1,018 436 (182 issues need help) 218 Updated Mar 13, 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 24 MIT 39 28 (2 issues need help) 8 Updated Mar 13, 2026
  • bacass Public

    Simple bacterial assembly and annotation pipeline

    nf-core/bacass’s past year of commit activity
    Nextflow 85 MIT 68 26 (1 issue needs help) 3 Updated Mar 13, 2026
  • genephylo Public
    nf-core/genephylo’s past year of commit activity
    Nextflow 0 MIT 1 6 1 Updated Mar 13, 2026
  • ribomsqc Public

    QC pipeline that monitors mass spectrometer performance in ribonucleoside analysis

    nf-core/ribomsqc’s past year of commit activity
    R 0 MIT 2 0 1 Updated Mar 13, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 86 MIT 285 136 39 Updated Mar 13, 2026
  • tools Public

    Python package with helper tools for the nf-core community.

    nf-core/tools’s past year of commit activity
    Python 295 MIT 230 330 48 Updated Mar 13, 2026
  • proteinfold Public

    Protein 3D structure prediction pipeline

    nf-core/proteinfold’s past year of commit activity
    HTML 99 MIT 64 78 (2 issues need help) 18 Updated Mar 13, 2026
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 27 MIT 4 6 7 Updated Mar 13, 2026
  • ops Public

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

    nf-core/ops’s past year of commit activity
    Python 3 3 37 22 Updated Mar 13, 2026
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