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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 261 206

  2. modules modules Public

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

    Nextflow 360 881

  3. rnaseq rnaseq Public

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

    Nextflow 1.1k 776

  4. sarek sarek Public

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

    Nextflow 458 454

  5. configs configs Public

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

    Nextflow 101 315

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 168 repositories
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 160 MIT 113 36 (4 issues need help) 5 Updated Jul 15, 2025
  • 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 156 MIT 53 38 (1 issue needs help) 6 Updated Jul 15, 2025
  • 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 458 MIT 454 293 (6 issues need help) 38 Updated Jul 15, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 76 MIT 245 88 10 Updated Jul 15, 2025
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 1 2 16 5 Updated Jul 15, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 261 MIT 206 272 36 Updated Jul 15, 2025
  • createtaxdb Public

    Parallelised and automated construction of metagenomic classifier databases of different tools

    nf-core/createtaxdb’s past year of commit activity
    Nextflow 14 MIT 9 6 0 Updated Jul 15, 2025
  • mhcquant Public

    Identify and quantify MHC eluted peptides from mass spectrometry raw data

    nf-core/mhcquant’s past year of commit activity
    Nextflow 36 MIT 29 7 (1 issue needs help) 6 Updated Jul 15, 2025
  • sopa Public

    Nextflow version of Sopa - spatial omics pipeline and analysis

    nf-core/sopa’s past year of commit activity
    Nextflow 1 MIT 1 0 0 Updated Jul 15, 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 360 MIT 881 428 (1 issue needs help) 176 Updated Jul 15, 2025
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