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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 280 220

  2. modules modules Public

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

    Nextflow 387 935

  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 813

  4. sarek sarek Public

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

    Nextflow 502 491

  5. configs configs Public

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

    Nextflow 104 335

  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
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 387 MIT 935 391 (1 issue needs help) 153 Updated Nov 19, 2025
  • mhcquant Public

    Identify and quantify MHC eluted peptides from mass spectrometry raw data

    nf-core/mhcquant’s past year of commit activity
    Nextflow 39 MIT 31 7 (1 issue needs help) 2 Updated Nov 19, 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 7 MIT 43 0 14 Updated Nov 19, 2025
  • tools Public

    Python package with helper tools for the nf-core community.

    nf-core/tools’s past year of commit activity
    Python 280 MIT 220 315 32 Updated Nov 19, 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 104 MIT 335 10 (1 issue needs help) 14 Updated Nov 19, 2025
  • tumourevo Public

    Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)

    nf-core/tumourevo’s past year of commit activity
    Nextflow 19 MIT 5 4 1 Updated Nov 19, 2025
  • seqinspector Public

    QC pipeline to inspect your sequences

    nf-core/seqinspector’s past year of commit activity
    Nextflow 14 MIT 35 45 (3 issues need help) 16 Updated Nov 19, 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 491 304 (6 issues need help) 38 Updated Nov 19, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 81 MIT 253 112 24 Updated Nov 19, 2025
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 94 MIT 27 11 7 Updated Nov 19, 2025
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