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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 324 257

  2. modules modules Public

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

    Nextflow 430 1.1k

  3. rnaseq rnaseq Public

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

    Nextflow 1.4k 901

  4. sarek sarek Public

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

    Nextflow 609 557

  5. configs configs Public

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

    Nextflow 113 375

  6. proposals proposals Public

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

    10 6

Repositories

Showing 10 of 201 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 430 MIT 1,109 304 (1 issue needs help) 174 Updated Oct 2, 2026
  • viralrecon Public

    Assembly and intrahost/low-frequency variant calling for viral samples

    nf-core/viralrecon's past year of commit activity
    Nextflow 166 MIT 159 58 (4 issues need help) 4 Updated Oct 2, 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 1,378 MIT 901 25 8 Updated Oct 2, 2026
  • raredisease Public

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

    nf-core/raredisease's past year of commit activity
    Nextflow 126 MIT 70 16 5 Updated Oct 2, 2026
  • 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 609 MIT 557 263 (5 issues need help) 43 Updated Oct 2, 2026
  • pacvar Public

    Longread PacBio sequencing processing for WGS and PureTarget

    nf-core/pacvar's past year of commit activity
    Nextflow 16 MIT 14 10 (1 issue needs help) 1 Updated Oct 2, 2026
  • proteinfamilies Public

    Generation and updating of protein families

    nf-core/proteinfamilies's past year of commit activity
    Nextflow 23 MIT 4 10 0 Updated Oct 2, 2026
  • datasync Public

    nf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks

    nf-core/datasync's past year of commit activity
    Nextflow 10 MIT 8 6 1 Updated Oct 2, 2026
  • diseasemodulediscovery Public

    A pipeline for network-based disease module identification.

    nf-core/diseasemodulediscovery's past year of commit activity
    Nextflow 6 MIT 6 38 12 Updated Oct 2, 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 95 MIT 68 85 (1 issue needs help) 10 Updated Oct 2, 2026
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