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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 328 266

  2. modules modules Public

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

    Nextflow 432 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 905

  4. sarek sarek Public

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

    Nextflow 614 562

  5. configs configs Public

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

    Nextflow 114 376

  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
  • modules Public

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

    nf-core/modules's past year of commit activity
    Nextflow 432 MIT 1,124 290 (1 issue needs help) 197 Updated Oct 18, 2026
  • circrna Public

    circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

    nf-core/circrna's past year of commit activity
    Nextflow 61 MIT 33 12 3 Updated Oct 18, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 99 MIT 301 125 30 Updated Oct 18, 2026
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    nf-core/scdownstream's past year of commit activity
    Nextflow 117 MIT 68 11 2 Updated Oct 18, 2026
  • taxprofiler Public

    Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

    nf-core/taxprofiler's past year of commit activity
    Nextflow 193 MIT 67 50 (1 issue needs help) 6 Updated Oct 18, 2026
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag's past year of commit activity
    Nextflow 323 MIT 160 78 (1 issue needs help) 8 Updated Oct 18, 2026
  • 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
    163 MIT 540 43 35 Updated Oct 18, 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 614 MIT 562 262 (5 issues need help) 50 Updated Oct 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 Oct 18, 2026
  • msproteomics Public
    nf-core/msproteomics's past year of commit activity
    Nextflow 0 MIT 1 0 1 Updated Oct 17, 2026
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