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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 260 203

  2. modules modules Public

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

    Nextflow 356 866

  3. rnaseq rnaseq Public

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

    Nextflow 1k 767

  4. sarek sarek Public

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

    Nextflow 451 447

  5. configs configs Public

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

    Nextflow 99 311

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 163 repositories
  • funcscan Public

    (Meta-)genome screening for functional and natural product gene sequences

    nf-core/funcscan’s past year of commit activity
    Nextflow 87 MIT 26 17 3 Updated Jun 12, 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
    130 MIT 410 33 15 Updated Jun 12, 2025
  • tfactivity Public

    Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

    nf-core/tfactivity’s past year of commit activity
    Nextflow 12 MIT 5 2 1 Updated Jun 12, 2025
  • proteinfamilies Public

    Generation and update of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 14 MIT 3 8 0 Updated Jun 12, 2025
  • createpanelrefs Public

    Generate Panel of Normals, models or other similar references from lots of samples

    nf-core/createpanelrefs’s past year of commit activity
    Nextflow 9 MIT 9 6 2 Updated Jun 12, 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 451 MIT 447 292 (6 issues need help) 38 Updated Jun 12, 2025
  • spatialvi Public

    Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

    nf-core/spatialvi’s past year of commit activity
    Nextflow 64 MIT 25 5 1 Updated Jun 12, 2025
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 100 MIT 45 37 5 Updated Jun 12, 2025
  • createtaxdb Public

    Parallelised and automated construction of metagenomic classifier databases of different tools

    nf-core/createtaxdb’s past year of commit activity
    Nextflow 9 MIT 7 7 1 Updated Jun 12, 2025
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 239 MIT 132 61 (1 issue needs help) 9 Updated Jun 12, 2025
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