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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 331 268

  2. modules modules Public

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

    Nextflow 436 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 911

  4. sarek sarek Public

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

    Nextflow 620 565

  5. configs configs Public

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

    Nextflow 114 380

  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
  • 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 11, 2026
  • smrnaseq Public

    A small-RNA sequencing analysis pipeline

    nf-core/smrnaseq's past year of commit activity
    Nextflow 103 MIT 140 22 (2 issues need help) 2 Updated Nov 11, 2026
  • bacass Public

    Simple bacterial assembly and annotation pipeline

    nf-core/bacass's past year of commit activity
    Nextflow 95 MIT 74 20 (1 issue needs help) 4 Updated Nov 10, 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 436 MIT 1,142 295 (1 issue needs help) 168 Updated Nov 10, 2026
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser's past year of commit activity
    Nextflow 129 MIT 45 15 8 Updated Nov 10, 2026
  • hadge Public

    Comprehensive pipeline for donor demultiplexing in single cell

    nf-core/hadge's past year of commit activity
    Nextflow 26 MIT 10 11 1 Updated Nov 10, 2026
  • demo Public

    nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.

    nf-core/demo's past year of commit activity
    Nextflow 16 MIT 27 3 7 Updated Nov 10, 2026
  • diseasemodulediscovery Public

    A pipeline for network-based disease module identification.

    nf-core/diseasemodulediscovery's past year of commit activity
    Nextflow 6 MIT 6 38 12 Updated Nov 10, 2026
  • methylseq Public

    Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair

    nf-core/methylseq's past year of commit activity
    Nextflow 201 MIT 185 27 7 Updated Nov 10, 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 3 22 11 Updated Nov 10, 2026
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