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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 275 215

  2. modules modules Public

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

    Nextflow 379 912

  3. rnaseq rnaseq Public

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

    Nextflow 1.1k 805

  4. sarek sarek Public

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

    Nextflow 494 486

  5. configs configs Public

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

    Nextflow 104 333

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 172 repositories
  • logos Public

    Host nf-core logos and templates for making new logos

    nf-core/logos’s past year of commit activity
    7 MIT 14 0 1 Updated Oct 28, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 81 MIT 253 103 25 Updated Oct 28, 2025
  • 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 36 MIT 18 20 2 Updated Oct 28, 2025
  • viralrecon Public

    Assembly and intrahost/low-frequency variant calling for viral samples

    nf-core/viralrecon’s past year of commit activity
    Nextflow 144 MIT 137 38 (3 issues need help) 9 Updated Oct 28, 2025
  • 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
    142 MIT 440 34 17 Updated Oct 28, 2025
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 248 MIT 141 66 (1 issue needs help) 10 Updated Oct 28, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 22 MIT 5 5 7 Updated Oct 28, 2025
  • isoseq Public

    Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

    nf-core/isoseq’s past year of commit activity
    Nextflow 48 MIT 21 9 1 Updated Oct 27, 2025
  • ops Public

    Different *Ops related scripts for the nf-core org.

    nf-core/ops’s past year of commit activity
    Python 3 2 37 16 Updated Oct 27, 2025
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 112 MIT 55 49 3 Updated Oct 27, 2025
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