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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 274 215

  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 804

  4. sarek sarek Public

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

    Nextflow 492 485

  5. configs configs Public

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

    Nextflow 104 332

  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
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 250 MIT 141 68 (1 issue needs help) 9 Updated Oct 24, 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 24, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 80 MIT 253 102 25 Updated Oct 24, 2025
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 379 MIT 912 383 (1 issue needs help) 141 Updated Oct 24, 2025
  • eager Public

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

    nf-core/eager’s past year of commit activity
    Nextflow 184 MIT 83 46 (2 issues need help) 9 Updated Oct 24, 2025
  • pixelator Public

    Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

    nf-core/pixelator’s past year of commit activity
    Nextflow 12 MIT 8 1 1 Updated Oct 24, 2025
  • seqsubmit Public

    nf-core pipeline for data submission to ENA

    nf-core/seqsubmit’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Oct 24, 2025
  • diseasemodulediscovery Public

    A pipeline for network-based disease module identification.

    nf-core/diseasemodulediscovery’s past year of commit activity
    Python 5 MIT 3 32 6 Updated Oct 24, 2025
  • 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 492 MIT 485 302 (6 issues need help) 36 Updated Oct 24, 2025
  • genomeqc Public

    Compare the quality of multiple genomes, along with their annotations.

    nf-core/genomeqc’s past year of commit activity
    Nextflow 17 MIT 16 55 (2 issues need help) 3 Updated Oct 24, 2025
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