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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 298 236

  2. modules modules Public

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

    Nextflow 408 1k

  3. rnaseq rnaseq Public

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

    Nextflow 1.3k 859

  4. sarek sarek Public

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

    Nextflow 557 525

  5. configs configs Public

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

    Nextflow 108 352

  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
  • 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 1,251 MIT 859 33 18 Updated Apr 13, 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 91 MIT 61 94 (1 issue needs help) 3 Updated Apr 13, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 91 MIT 285 118 28 Updated Apr 13, 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 408 MIT 1,032 315 (65 issues need help) 171 Updated Apr 13, 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 352 12 (1 issue needs help) 34 Updated Apr 13, 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 24 Updated Apr 13, 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 45 (1 issue needs help) 6 Updated Apr 13, 2026
  • createtaxdb Public

    Parallelised and automated construction of metagenomic classifier databases of different tools

    nf-core/createtaxdb’s past year of commit activity
    Nextflow 20 MIT 10 9 1 Updated Apr 13, 2026
  • riboseq Public

    Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.

    nf-core/riboseq’s past year of commit activity
    Nextflow 25 MIT 18 16 5 Updated Apr 13, 2026
  • bacass Public

    Simple bacterial assembly and annotation pipeline

    nf-core/bacass’s past year of commit activity
    Nextflow 85 MIT 69 27 (1 issue needs help) 4 Updated Apr 13, 2026
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