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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 355 840

  3. rnaseq rnaseq Public

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

    Nextflow 1k 752

  4. sarek sarek Public

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

    Nextflow 441 443

  5. configs configs Public

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

    Nextflow 99 306

  6. proposals proposals Public

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

    8

Repositories

Showing 10 of 160 repositories
  • proteinfamilies Public

    Generation and update of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 13 MIT 2 13 0 Updated Apr 30, 2025
  • testpipeline Public

    A small example pipeline used to test new nf-core infrastructure and common code.

    nf-core/testpipeline’s past year of commit activity
    Nextflow 5 MIT 41 0 9 Updated Apr 30, 2025
  • 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
    122 MIT 395 33 10 Updated Apr 30, 2025
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 66 MIT 18 28 6 Updated Apr 30, 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 30, 2025
  • nascent Public

    Nascent Transcription Processing Pipeline

    nf-core/nascent’s past year of commit activity
    Nextflow 19 MIT 11 40 4 Updated Apr 30, 2025
  • airrflow Public

    B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

    nf-core/airrflow’s past year of commit activity
    Nextflow 60 MIT 42 24 5 Updated Apr 30, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 2 2 31 10 Updated Apr 30, 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 Apr 30, 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 840 484 (1 issue needs help) 179 Updated Apr 29, 2025
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