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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 295 230

  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 855

  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
  • 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 1,024 351 (97 issues need help) 180 Updated Mar 16, 2026
  • genephylomodeler Public

    A bioinformatics pipeline that fits evolutionary models and performs hypothesis testing on multiple sequence alignments

    nf-core/genephylomodeler’s past year of commit activity
    Nextflow 0 MIT 0 2 0 Updated Mar 16, 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 855 31 16 Updated Mar 16, 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 48 6 Updated Mar 16, 2026
  • differentialabundance Public

    Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

    nf-core/differentialabundance’s past year of commit activity
    Nextflow 90 MIT 59 89 (1 issue needs help) 8 Updated Mar 16, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 86 MIT 285 126 32 Updated Mar 16, 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 33 2 0 Updated Mar 16, 2026
  • slackbot Public
    nf-core/slackbot’s past year of commit activity
    Python 0 0 0 0 Updated Mar 16, 2026
  • longraredisease Public

    Long read sequencing pipeline to identify variants in patients with neurodevelopmental disorders

    nf-core/longraredisease’s past year of commit activity
    Nextflow 7 MIT 3 0 1 Updated Mar 16, 2026
  • ops Public

    Different *Ops related scripts for the nf-core org.

    nf-core/ops’s past year of commit activity
    Python 3 3 37 23 Updated Mar 16, 2026
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