Skip to content
@nf-core

nf-core

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

Pinned Loading

  1. tools tools Public

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

    Python 256 201

  2. modules modules Public

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

    Nextflow 355 838

  3. rnaseq rnaseq Public

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

    Nextflow 1k 752

  4. sarek sarek Public

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

    Nextflow 441 443

  5. configs configs Public

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

    Nextflow 98 305

  6. proposals proposals Public

    Where new ideas for nf-core pipelines and more are proposed

    8

Repositories

Showing 10 of 160 repositories
  • configs Public

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

    nf-core/configs’s past year of commit activity
    Nextflow 98 MIT 305 9 17 Updated Apr 25, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 17 MIT 6 5 5 Updated Apr 25, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 75 MIT 245 95 25 Updated Apr 25, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 256 MIT 201 272 32 Updated Apr 25, 2025
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    nf-core/demultiplex’s past year of commit activity
    Nextflow 46 MIT 43 22 1 Updated Apr 24, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 2 2 30 10 Updated Apr 24, 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 355 MIT 838 486 (1 issue needs help) 176 Updated Apr 24, 2025
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 153 MIT 112 31 (4 issues need help) 2 Updated Apr 24, 2025
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    nf-core/scdownstream’s past year of commit activity
    Nextflow 54 MIT 23 25 (3 issues need help) 1 Updated Apr 24, 2025
  • methylong Public

    Extract methylation calls from long reads (ONT/ PacBio)

    nf-core/methylong’s past year of commit activity
    5 MIT 1 1 2 Updated Apr 24, 2025

Top languages

Loading…

Most used topics

Loading…