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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 301 239

  2. modules modules Public

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

    Nextflow 412 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 862

  4. sarek sarek Public

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

    Nextflow 561 526

  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
  • 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 4 0 0 Updated Apr 22, 2026
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 106 MIT 28 15 6 Updated Apr 22, 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 412 MIT 1,037 304 (45 issues need help) 181 Updated Apr 22, 2026
  • stats Public
    nf-core/stats’s past year of commit activity
    Python 2 3 36 5 Updated Apr 21, 2026
  • hlatyping Public

    Precision HLA typing from next-generation sequencing data

    nf-core/hlatyping’s past year of commit activity
    Nextflow 79 MIT 37 11 2 Updated Apr 21, 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 1,264 MIT 862 21 10 Updated Apr 21, 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 3 Updated Apr 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 45 MIT 27 23 (3 issues need help) 3 Updated Apr 21, 2026
  • sarek Public

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

    nf-core/sarek’s past year of commit activity
    Nextflow 561 MIT 526 238 (5 issues need help) 38 Updated Apr 21, 2026
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 301 MIT 239 331 47 Updated Apr 21, 2026
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