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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 256 201

  2. modules modules Public

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

    Nextflow 354 837

  3. rnaseq rnaseq Public

    RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

    Nextflow 1k 747

  4. sarek sarek Public

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

    Nextflow 441 440

  5. configs configs Public

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

    Nextflow 98 303

  6. proposals proposals Public

    Where new ideas for nf-core pipelines and more are proposed

    7

Repositories

Showing 10 of 158 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 354 MIT 837 504 (1 issue needs help) 179 Updated Apr 21, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 75 MIT 246 95 27 Updated Apr 21, 2025
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    nf-core/demultiplex’s past year of commit activity
    Nextflow 46 MIT 43 22 2 Updated Apr 20, 2025
  • references Public

    nf-core/references is a bioinformatics pipeline that build references, for multiple use cases

    nf-core/references’s past year of commit activity
    Nextflow 14 MIT 5 23 3 Updated Apr 20, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 2 2 30 10 Updated Apr 20, 2025
  • references-datasheets Public
    nf-core/references-datasheets’s past year of commit activity
    Shell 1 MIT 1 0 0 Updated Apr 20, 2025
  • pathogensurveillance Public

    Surveillance of pathogens using population genomics and sequencing

    nf-core/pathogensurveillance’s past year of commit activity
    Nextflow 22 MIT 7 54 (3 issues need help) 2 Updated Apr 18, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 17 MIT 6 5 5 Updated Apr 18, 2025
  • tfactivity Public

    Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

    nf-core/tfactivity’s past year of commit activity
    Nextflow 12 MIT 4 1 0 Updated Apr 17, 2025
  • genomeqc Public

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

    nf-core/genomeqc’s past year of commit activity
    Nextflow 10 MIT 16 50 (2 issues need help) 4 Updated Apr 17, 2025
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