Skip to content
@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.
README.md

Pinned Loading

  1. tools tools Public

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

    Python 328 266

  2. modules modules Public

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

    Nextflow 433 1.1k

  3. rnaseq rnaseq Public

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

    Nextflow 1.4k 908

  4. sarek sarek Public

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

    Nextflow 614 564

  5. configs configs Public

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

    Nextflow 114 377

  6. proposals proposals Public

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

    10 6

Repositories

Showing 10 of 203 repositories
  • diseasemodulediscovery Public

    A pipeline for network-based disease module identification.

    nf-core/diseasemodulediscovery's past year of commit activity
    Nextflow 6 MIT 6 38 12 Updated Oct 21, 2026
  • rnasplice Public

    rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

    nf-core/rnasplice's past year of commit activity
    Nextflow 70 MIT 43 5 0 Updated Oct 21, 2026
  • spatialaxe Public

    A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data

    nf-core/spatialaxe's past year of commit activity
    Python 46 MIT 26 49 12 Updated Oct 21, 2026
  • variantbenchmarking Public

    Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research

    nf-core/variantbenchmarking's past year of commit activity
    Nextflow 52 MIT 33 28 (3 issues need help) 4 Updated Oct 21, 2026
  • references Public

    nf-core/references is a bioinformatics pipeline that build references, for multiple use cases

    nf-core/references's past year of commit activity
    Nextflow 23 MIT 6 26 1 Updated Oct 21, 2026
  • dartseq Public

    Pipeline for m6A detection in RNAseq data

    nf-core/dartseq's past year of commit activity
    Nextflow 0 MIT 2 3 (2 issues need help) 3 Updated Oct 21, 2026
  • raredisease Public

    Call and score variants from WGS/WES of rare disease patients.

    nf-core/raredisease's past year of commit activity
    Nextflow 126 MIT 71 12 7 Updated Oct 21, 2026
  • 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 61 MIT 33 10 2 Updated Oct 21, 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 433 MIT 1,125 287 (1 issue needs help) 194 Updated Oct 21, 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 5 0 0 Updated Oct 21, 2026
View all repositories