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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 256 201

  2. modules modules Public

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

    Nextflow 352 836

  3. rnaseq rnaseq Public

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

    Nextflow 1k 748

  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 98 301

  6. proposals proposals Public

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

    6

Repositories

Showing 10 of 158 repositories
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 75 MIT 245 94 25 Updated Apr 12, 2025
  • reportho Public

    nf-core pipeline for comparative analysis of ortholog predictions

    nf-core/reportho’s past year of commit activity
    Nextflow 11 MIT 6 6 2 Updated Apr 12, 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 836 512 (1 issue needs help) 176 Updated Apr 12, 2025
  • methylarray Public

    Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.

    nf-core/methylarray’s past year of commit activity
    Nextflow 4 MIT 3 12 1 Updated Apr 12, 2025
  • methylseq Public

    Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

    nf-core/methylseq’s past year of commit activity
    Nextflow 165 MIT 153 26 (1 issue needs help) 8 Updated Apr 12, 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 27 6 Updated Apr 11, 2025
  • fastquorum Public

    Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

    nf-core/fastquorum’s past year of commit activity
    Nextflow 23 MIT 13 11 (1 issue needs help) 0 Updated Apr 11, 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 30 (3 issues need help) 3 Updated Apr 11, 2025
  • test-datasets Public

    Test data to be used for automated testing with the nf-core pipelines

    nf-core/test-datasets’s past year of commit activity
    121 MIT 392 33 13 Updated Apr 11, 2025
  • 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 1,013 MIT 748 85 15 Updated Apr 11, 2025
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