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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 297 234

  2. modules modules Public

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

    Nextflow 406 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 856

  4. sarek sarek Public

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

    Nextflow 555 526

  5. configs configs Public

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

    Nextflow 108 351

  6. proposals proposals Public

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

    8 4

Repositories

Showing 10 of 188 repositories
  • strict-syntax-health Public

    Track Nextflow strict syntax linting health across nf-core pipelines

    nf-core/strict-syntax-health’s past year of commit activity
    Python 7 MIT 3 0 0 Updated Mar 29, 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 91 MIT 61 37 (3 issues need help) 7 Updated Mar 28, 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 24 Updated Mar 28, 2026
  • proteinannotator Public

    Generation of sequence-level annotations for amino acid sequences

    nf-core/proteinannotator’s past year of commit activity
    Nextflow 11 MIT 11 22 8 Updated Mar 28, 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 72 MIT 32 2 1 Updated Mar 28, 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 406 MIT 1,029 336 (81 issues need help) 204 Updated Mar 28, 2026
  • stats Public
    nf-core/stats’s past year of commit activity
    Python 2 3 36 4 Updated Mar 28, 2026
  • taxprofiler Public

    Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

    nf-core/taxprofiler’s past year of commit activity
    Nextflow 184 MIT 64 43 (1 issue needs help) 6 Updated Mar 28, 2026
  • msproteomics Public
    nf-core/msproteomics’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Mar 28, 2026
  • funcprofiler Public

    Read-based functional profiling of microbiome sequencing data

    nf-core/funcprofiler’s past year of commit activity
    Nextflow 2 MIT 3 12 1 Updated Mar 28, 2026
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