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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 248 196

  2. modules modules Public

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

    Nextflow 294 754

  3. rnaseq rnaseq Public

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

    Nextflow 991 731

  4. sarek sarek Public

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

    Nextflow 426 430

Repositories

Showing 10 of 155 repositories
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 61 MIT 15 23 2 Updated Mar 13, 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 294 MIT 754 532 (9 issues need help) 113 Updated Mar 13, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 72 MIT 230 91 29 Updated Mar 13, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 248 MIT 196 267 36 Updated Mar 13, 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 5 Updated Mar 13, 2025
  • fastquorum Public

    Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

    nf-core/fastquorum’s past year of commit activity
    Nextflow 21 MIT 12 15 (1 issue needs help) 3 Updated Mar 12, 2025
  • metatdenovo Public

    Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

    nf-core/metatdenovo’s past year of commit activity
    Nextflow 27 MIT 12 7 1 Updated Mar 12, 2025
  • references Public

    nf-core/references is a bioinformatics pipeline that build references, for multiple use cases

    nf-core/references’s past year of commit activity
    Nextflow 11 MIT 4 17 0 Updated Mar 12, 2025
  • 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 74 MIT 43 63 (1 issue needs help) 5 Updated Mar 12, 2025
  • proteinannotator Public

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

    nf-core/proteinannotator’s past year of commit activity
    Nextflow 0 MIT 0 1 0 Updated Mar 12, 2025
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