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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 247 194

  2. modules modules Public

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

    Nextflow 292 751

  3. rnaseq rnaseq Public

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

    Nextflow 984 722

  4. sarek sarek Public

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

    Nextflow 422 428

  5. chipseq chipseq Public

    ChIP-seq peak-calling, QC and differential analysis pipeline.

    Nextflow 206 149

  6. eager eager Public

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

    Nextflow 159 81

Repositories

Showing 10 of 153 repositories
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 69 MIT 216 91 33 Updated Feb 17, 2025
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 59 MIT 14 16 2 Updated Feb 17, 2025
  • coproid Public

    Coprolite host Identification pipeline

    nf-core/coproid’s past year of commit activity
    Nextflow 9 MIT 4 2 2 Updated Feb 17, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 33 8 Updated Feb 16, 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
    115 MIT 367 31 15 Updated Feb 16, 2025
  • multiplesequencealign Public

    A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.

    nf-core/multiplesequencealign’s past year of commit activity
    Nextflow 26 MIT 12 6 2 Updated Feb 15, 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 292 MIT 751 464 (1 issue needs help) 194 Updated Feb 15, 2025
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 0 2 15 10 Updated Feb 15, 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 11 MIT 4 16 0 Updated Feb 14, 2025
  • genomeassembler Public
    nf-core/genomeassembler’s past year of commit activity
    Nextflow 17 MIT 13 1 1 Updated Feb 14, 2025
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