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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 300 238

  2. modules modules Public

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

    Nextflow 410 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 559 526

  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
  • 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 1,260 MIT 860 24 8 Updated Apr 18, 2026
  • diseasemodulediscovery Public

    A pipeline for network-based disease module identification.

    nf-core/diseasemodulediscovery’s past year of commit activity
    Python 5 MIT 4 37 8 Updated Apr 18, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 91 MIT 287 119 33 Updated Apr 18, 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 2 Updated Apr 18, 2026
  • setup-nf-test Public
    nf-core/setup-nf-test’s past year of commit activity
    JavaScript 7 MIT 3 1 2 Updated Apr 18, 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 20 Updated Apr 18, 2026
  • magmap Public

    Best-practice analysis pipeline for mapping reads to a (large) collections of genomes

    nf-core/magmap’s past year of commit activity
    Nextflow 10 MIT 6 6 1 Updated Apr 18, 2026
  • 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 18, 2026
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 300 MIT 238 329 48 Updated Apr 17, 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 410 MIT 1,036 307 (54 issues need help) 178 Updated Apr 17, 2026
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