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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 253 201

  2. modules modules Public

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

    Nextflow 352 834

  3. rnaseq rnaseq Public

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

    Nextflow 1k 747

  4. sarek sarek Public

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

    Nextflow 439 439

  5. configs configs Public

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

    Nextflow 98 300

  6. proposals proposals Public

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

    4

Repositories

Showing 10 of 158 repositories
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 17 MIT 6 5 6 Updated Apr 7, 2025
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 65 MIT 17 26 3 Updated Apr 6, 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 352 MIT 834 525 (1 issue needs help) 174 Updated Apr 6, 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 24 28 (3 issues need help) 3 Updated Apr 6, 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 27 Updated Apr 6, 2025
  • genomeqc Public

    Compare the quality of multiple genomes, along with their annotations.

    nf-core/genomeqc’s past year of commit activity
    Nextflow 10 MIT 16 38 (2 issues need help) 7 Updated Apr 6, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 253 MIT 201 269 33 Updated Apr 5, 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 77 MIT 45 61 (1 issue needs help) 5 Updated Apr 4, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 2 2 40 10 Updated Apr 4, 2025
  • proteinfold Public

    Protein 3D structure prediction pipeline

    nf-core/proteinfold’s past year of commit activity
    Nextflow 78 MIT 55 39 (2 issues need help) 8 Updated Apr 4, 2025
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