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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 297 234

  2. modules modules Public

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

    Nextflow 406 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 556 526

  5. configs configs Public

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

    Nextflow 108 350

  6. proposals proposals Public

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

    8 4

Repositories

Showing 10 of 188 repositories
  • methylong Public

    Extract methylation calls from long reads (ONT/ PacBio)

    nf-core/methylong’s past year of commit activity
    Nextflow 23 MIT 6 2 1 Updated Mar 31, 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 184 MIT 64 43 (1 issue needs help) 7 Updated Mar 31, 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 406 MIT 1,029 336 (81 issues need help) 197 Updated Mar 31, 2026
  • ampliseq Public

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    nf-core/ampliseq’s past year of commit activity
    Nextflow 239 MIT 150 22 2 Updated Mar 31, 2026
  • 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 108 MIT 350 12 (1 issue needs help) 26 Updated Mar 31, 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 27 (1 issue needs help) 3 Updated Mar 31, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 88 MIT 284 116 32 Updated Mar 31, 2026
  • 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
    157 MIT 486 38 24 Updated Mar 31, 2026
  • 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 72 MIT 32 2 1 Updated Mar 31, 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 8 MIT 6 4 2 Updated Mar 31, 2026
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