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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 293 224

  2. modules modules Public

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

    Nextflow 402 970

  3. rnaseq rnaseq Public

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

    Nextflow 1.2k 851

  4. sarek sarek Public

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

    Nextflow 553 526

  5. configs configs Public

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

    Nextflow 107 344

  6. proposals proposals Public

    Where new ideas for nf-core pipelines, special interest groups and more are proposed

    8 4

Repositories

Showing 10 of 183 repositories
  • mhcquant Public

    Identify and quantify MHC eluted peptides from mass spectrometry raw data

    nf-core/mhcquant’s past year of commit activity
    Nextflow 44 MIT 33 14 (1 issue needs help) 1 Updated Mar 4, 2026
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 293 MIT 224 334 44 Updated Mar 4, 2026
  • taxprofiler Public

    Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

    nf-core/taxprofiler’s past year of commit activity
    Nextflow 179 MIT 61 46 (1 issue needs help) 9 Updated Mar 4, 2026
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 114 MIT 59 47 7 Updated Mar 4, 2026
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 402 MIT 970 435 (110 issues need help) 143 Updated Mar 4, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 85 MIT 274 115 37 Updated Mar 4, 2026
  • proteinfamilies Public

    Generation and updating of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 23 MIT 3 7 0 Updated Mar 4, 2026
  • pixelator Public

    Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

    nf-core/pixelator’s past year of commit activity
    Nextflow 13 MIT 9 2 0 Updated Mar 4, 2026
  • seqinspector Public

    Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.

    nf-core/seqinspector’s past year of commit activity
    Nextflow 22 MIT 38 23 (2 issues need help) 8 Updated Mar 4, 2026
  • proteinfold Public

    Protein 3D structure prediction pipeline

    nf-core/proteinfold’s past year of commit activity
    HTML 99 MIT 61 55 (2 issues need help) 7 Updated Mar 4, 2026
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