Skip to content
@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.
README.md

Pinned Loading

  1. tools tools Public

    Python package with helper tools for the nf-core community.

    Python 252 201

  2. modules modules Public

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

    Nextflow 348 827

  3. rnaseq rnaseq Public

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

    Nextflow 1k 746

  4. sarek sarek Public

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

    Nextflow 434 437

Repositories

Showing 10 of 158 repositories
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 62 MIT 16 24 3 Updated Mar 28, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 74 MIT 243 97 26 Updated Mar 28, 2025
  • dualrnaseq Public

    Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

    nf-core/dualrnaseq’s past year of commit activity
    Nextflow 21 MIT 35 16 9 Updated Mar 28, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 15 MIT 6 5 6 Updated Mar 28, 2025
  • proteinannotator Public

    The best protein annotation pipeline in the world. Protein fasta → ??? → Annotations

    nf-core/proteinannotator’s past year of commit activity
    Nextflow 1 MIT 3 8 4 Updated Mar 28, 2025
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 348 MIT 827 529 (1 issue needs help) 172 Updated Mar 27, 2025
  • viralrecon Public

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

    nf-core/viralrecon’s past year of commit activity
    Nextflow 133 MIT 125 30 (4 issues need help) 10 Updated Mar 27, 2025
  • genomeqc Public

    Compare the quality of multiple genomes, along with their annotations.

    nf-core/genomeqc’s past year of commit activity
    Nextflow 8 MIT 16 41 (3 issues need help) 6 Updated Mar 27, 2025
  • scrnaseq Public

    Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

    nf-core/scrnaseq’s past year of commit activity
    Nextflow 260 MIT 186 59 (1 issue needs help) 5 Updated Mar 27, 2025
  • reportho Public

    nf-core pipeline for comparative analysis of ortholog predictions

    nf-core/reportho’s past year of commit activity
    Nextflow 10 MIT 6 5 0 Updated Mar 27, 2025
View all repositories