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@nf-core

nf-core

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

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  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 355 840

  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 99 306

  6. proposals proposals Public

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

    8

Repositories

Showing 10 of 160 repositories
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 153 MIT 112 28 (4 issues need help) 1 Updated Apr 29, 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 840 484 (1 issue needs help) 177 Updated Apr 29, 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 29, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 2 2 30 10 Updated Apr 28, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 75 MIT 246 95 26 Updated Apr 28, 2025
  • spatialxe Public
    nf-core/spatialxe’s past year of commit activity
    Nextflow 17 MIT 8 27 4 Updated Apr 28, 2025
  • logos Public

    Host nf-core logos and templates for making new logos

    nf-core/logos’s past year of commit activity
    6 MIT 13 0 0 Updated Apr 28, 2025
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 235 MIT 125 63 (1 issue needs help) 10 Updated Apr 28, 2025
  • ampliseq Public

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    nf-core/ampliseq’s past year of commit activity
    Nextflow 200 MIT 135 20 3 Updated Apr 28, 2025
  • epitopeprediction Public

    A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

    nf-core/epitopeprediction’s past year of commit activity
    Nextflow 44 MIT 24 21 3 Updated Apr 28, 2025

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