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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 355 845

  3. rnaseq rnaseq Public

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

    Nextflow 1k 755

  4. sarek sarek Public

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

    Nextflow 440 443

  5. configs configs Public

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

    Nextflow 99 307

  6. proposals proposals Public

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

    8

Repositories

Showing 10 of 161 repositories
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 69 MIT 19 30 7 Updated May 7, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 76 MIT 246 95 27 Updated May 7, 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 May 7, 2025
  • nascent Public

    Nascent Transcription Processing Pipeline

    nf-core/nascent’s past year of commit activity
    Nextflow 19 MIT 11 39 3 Updated May 7, 2025
  • configs Public

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

    nf-core/configs’s past year of commit activity
    Nextflow 99 MIT 307 8 11 Updated May 7, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 2 2 31 10 Updated May 7, 2025
  • pathogensurveillance Public

    Surveillance of pathogens using population genomics and sequencing

    nf-core/pathogensurveillance’s past year of commit activity
    Nextflow 22 MIT 7 57 (3 issues need help) 2 Updated May 7, 2025
  • raredisease Public

    Call and score variants from WGS/WES of rare disease patients.

    nf-core/raredisease’s past year of commit activity
    Nextflow 100 MIT 44 37 6 Updated May 6, 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 355 MIT 845 482 (1 issue needs help) 176 Updated May 7, 2025
  • variantbenchmarking Public

    Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research

    nf-core/variantbenchmarking’s past year of commit activity
    Nextflow 28 MIT 14 23 1 Updated May 6, 2025
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