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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 295 232

  2. modules modules Public

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

    Nextflow 404 1k

  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 856

  4. sarek sarek Public

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

    Nextflow 555 526

  5. configs configs Public

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

    Nextflow 108 348

  6. proposals proposals Public

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

    8 4

Repositories

Showing 10 of 185 repositories
  • 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
    153 MIT 480 38 22 Updated Mar 18, 2026
  • 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 75 MIT 50 33 2 Updated Mar 18, 2026
  • eager Public

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

    nf-core/eager’s past year of commit activity
    Nextflow 200 MIT 88 47 (2 issues need help) 6 Updated Mar 18, 2026
  • proteinfold Public

    Protein 3D structure prediction pipeline

    nf-core/proteinfold’s past year of commit activity
    HTML 99 MIT 64 75 (2 issues need help) 14 Updated Mar 18, 2026
  • rnaseq Public

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

    nf-core/rnaseq’s past year of commit activity
    Nextflow 1,230 MIT 856 31 16 Updated Mar 18, 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 404 MIT 1,025 347 (94 issues need help) 176 Updated Mar 18, 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 60 47 6 Updated Mar 18, 2026
  • drop Public

    Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

    nf-core/drop’s past year of commit activity
    Nextflow 7 MIT 6 5 3 Updated Mar 18, 2026
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    nf-core/demultiplex’s past year of commit activity
    Nextflow 54 MIT 52 23 2 Updated Mar 18, 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 24 MIT 39 25 (1 issue needs help) 5 Updated Mar 18, 2026
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