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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 557 526

  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
  • funcprofiler Public

    Read-based functional profiling of microbiome sequencing data

    nf-core/funcprofiler’s past year of commit activity
    Nextflow 2 MIT 3 12 2 Updated Apr 14, 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 1,033 313 (62 issues need help) 179 Updated Apr 14, 2026
  • circdna Public

    Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

    nf-core/circdna’s past year of commit activity
    Python 31 MIT 16 10 0 Updated Apr 14, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 91 MIT 286 118 33 Updated Apr 14, 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) 8 Updated Apr 14, 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 1,253 MIT 859 28 16 Updated Apr 14, 2026
  • lsmquant Public

    A pipeline for processing and analysis of light-sheet microscopy images.

    nf-core/lsmquant’s past year of commit activity
    Nextflow 6 MIT 3 1 0 Updated Apr 14, 2026
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    nf-core/demultiplex’s past year of commit activity
    Nextflow 54 MIT 52 19 0 Updated Apr 14, 2026
  • metapep Public

    From metagenomes to epitopes and beyond

    nf-core/metapep’s past year of commit activity
    Nextflow 12 MIT 8 15 2 Updated Apr 14, 2026
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 29 MIT 5 6 10 Updated Apr 14, 2026
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