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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 329 268

  2. modules modules Public

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

    Nextflow 434 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 910

  4. sarek sarek Public

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

    Nextflow 616 565

  5. configs configs Public

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

    Nextflow 114 378

  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
  • 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 616 MIT 565 246 (5 issues need help) 50 Updated Nov 1, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 100 MIT 301 125 33 Updated Nov 1, 2026
  • tools Public

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

    nf-core/tools's past year of commit activity
    Python 329 MIT 268 369 97 Updated Nov 1, 2026
  • stats Public

    nf-core in numbers

    nf-core/stats's past year of commit activity
    Python 2 4 45 15 Updated Nov 1, 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 434 MIT 1,131 291 (1 issue needs help) 205 Updated Nov 1, 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 Nov 1, 2026
  • nf-core-utils Public

    Nextflow plugin with nf-core utility functions

    nf-core/nf-core-utils's past year of commit activity
    Groovy 1 Apache-2.0 1 21 5 Updated Oct 31, 2026
  • scrnaseq Public

    Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

    nf-core/scrnaseq's past year of commit activity
    Nextflow 364 MIT 234 61 (1 issue needs help) 7 Updated Oct 31, 2026
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag's past year of commit activity
    Nextflow 326 MIT 162 79 (1 issue needs help) 7 Updated Oct 31, 2026
  • seqinspector Public

    Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.

    nf-core/seqinspector's past year of commit activity
    Nextflow 28 MIT 47 27 3 Updated Oct 31, 2026
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