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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 281 220

  2. modules modules Public

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

    Nextflow 387 936

  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 815

  4. sarek sarek Public

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

    Nextflow 502 490

  5. configs configs Public

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

    Nextflow 104 336

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 173 repositories
  • phaseimpute Public

    A bioinformatics pipeline to phase and impute genetic data

    nf-core/phaseimpute’s past year of commit activity
    Nextflow 25 MIT 21 17 11 Updated Nov 20, 2025
  • smrnaseq Public

    A small-RNA sequencing analysis pipeline

    nf-core/smrnaseq’s past year of commit activity
    Nextflow 97 MIT 130 16 (1 issue needs help) 2 Updated Nov 20, 2025
  • deepmutscan Public

    nf-core/deepmutscan is a reproducible, scalable, and community-curated pipeline for analyzing deep mutational scanning (DMS) data using shotgun DNA sequencing.

    nf-core/deepmutscan’s past year of commit activity
    Nextflow 3 MIT 3 0 4 Updated Nov 20, 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 502 MIT 490 304 (6 issues need help) 38 Updated Nov 20, 2025
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 2 3 38 7 Updated Nov 20, 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 18 Updated Nov 20, 2025
  • rnavar Public

    gatk4 RNA variant calling pipeline

    nf-core/rnavar’s past year of commit activity
    Nextflow 55 MIT 42 18 2 Updated Nov 20, 2025
  • drugresponseeval Public

    Pipeline for testing drug response prediction models in a statistically and biologically sound way.

    nf-core/drugresponseeval’s past year of commit activity
    Nextflow 24 MIT 6 9 1 Updated Nov 20, 2025
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    nf-core/demultiplex’s past year of commit activity
    Nextflow 51 MIT 46 25 0 Updated Nov 20, 2025
  • createtaxdb Public

    Parallelised and automated construction of metagenomic classifier databases of different tools

    nf-core/createtaxdb’s past year of commit activity
    Nextflow 17 MIT 10 7 0 Updated Nov 20, 2025
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