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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 405 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 108 350

  6. proposals proposals Public

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

    8 4

Repositories

Showing 10 of 187 repositories
  • msproteomics Public
    nf-core/msproteomics’s past year of commit activity
    Nextflow 0 MIT 1 0 0 Updated Mar 25, 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 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 405 MIT 1,027 331 (82 issues need help) 195 Updated Mar 25, 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 319 MIT 214 77 (1 issue needs help) 11 Updated Mar 25, 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 0 Updated Mar 25, 2026
  • seqsubmit Public

    nf-core pipeline for data submission to ENA

    nf-core/seqsubmit’s past year of commit activity
    Nextflow 3 MIT 4 12 2 Updated Mar 25, 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 25, 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 27 (1 issue needs help) 4 Updated Mar 25, 2026
  • genomicrelatedness Public

    Bioinformatics pipeline for estimating genetic relatedness from low-coverage whole-genome sequencing (sWGS) data

    nf-core/genomicrelatedness’s past year of commit activity
    Nextflow 2 MIT 3 0 0 Updated Mar 25, 2026
  • configs Public

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

    nf-core/configs’s past year of commit activity
    Nextflow 108 MIT 350 12 (1 issue needs help) 29 Updated Mar 25, 2026
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