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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 300 239

  2. modules modules Public

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

    Nextflow 411 1k

  3. rnaseq rnaseq Public

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

    Nextflow 1.3k 860

  4. sarek sarek Public

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

    Nextflow 560 526

  5. configs configs Public

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

    Nextflow 108 353

  6. proposals proposals Public

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

    9 4

Repositories

Showing 10 of 188 repositories
  • airrflow Public

    B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

    nf-core/airrflow’s past year of commit activity
    Nextflow 75 MIT 52 34 3 Updated Apr 20, 2026
  • 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 1,263 MIT 860 25 11 Updated Apr 20, 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 411 MIT 1,036 306 (50 issues need help) 186 Updated Apr 20, 2026
  • differentialabundance Public

    Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

    nf-core/differentialabundance’s past year of commit activity
    Nextflow 92 MIT 61 93 (1 issue needs help) 5 Updated Apr 20, 2026
  • setup-nf-test Public
    nf-core/setup-nf-test’s past year of commit activity
    JavaScript 7 MIT 3 1 2 Updated Apr 20, 2026
  • circdna Public

    Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

    nf-core/circdna’s past year of commit activity
    Python 31 MIT 16 10 0 Updated Apr 20, 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 42 (1 issue needs help) 6 Updated Apr 20, 2026
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 116 MIT 63 55 9 Updated Apr 20, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 91 MIT 288 118 30 Updated Apr 20, 2026
  • 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
    161 MIT 496 40 31 Updated Apr 20, 2026
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