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@nf-cmgg Center For Medical Genetics Ghent - Nextflow workflows

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    11 repositories

    • smallvariants

      Public
      A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
      annotationngsgermlinecramngs-pipelinegenotypinggermline-variant-callingshort-reads
      Nextflow
      •
      MIT License
      •5•13•14•3•Updated Jan 7, 2026Jan 7, 2026

    • test-datasets

      Public
      Test datasets for unit tests with the nf-cmgg pipelines
      Python
      •
      MIT License
      •3•0•0•0•Updated Jan 6, 2026Jan 6, 2026

    • preprocessing

      Public
      Preprocessing workflow for sequencing data at CMGG
      Nextflow
      •
      MIT License
      •6•5•8•2•Updated Dec 23, 2025Dec 23, 2025

    • report

      Public
      A post-processing reporting pipeline for internal use at CMGG
      Nextflow
      •
      MIT License
      •3•0•0•3•Updated Dec 16, 2025Dec 16, 2025

    • structural

      Public
      A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads
      annotationrepeatsngscnvcramstructural-variationngs-pipelinenextflow-pipelineshort-reads
      Nextflow
      •
      MIT License
      •2•26•16•2•Updated Dec 12, 2025Dec 12, 2025

    • exomecnv

      Public
      A nextflow pipeline for calling exome CNVs
      Nextflow
      •
      MIT License
      •4•11•4•1•Updated Dec 10, 2025Dec 10, 2025

    • configs

      Public
      Nextflow config files
      MIT License
      •1•0•0•1•Updated Dec 2, 2025Dec 2, 2025

    • wisecondorx

      Public
      A nextflow pipeline for creating references for WisecondorX
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Nov 18, 2025Nov 18, 2025

    • sampletracking

      Public
      CMGG Sampletracking workflow
      Nextflow
      •
      MIT License
      •2•0•4•1•Updated Nov 14, 2025Nov 14, 2025

    • nextflow-beginner-feb-2024

      Public
      The repository used at the Beginner Nextflow course in february 2024
      Nextflow
      •
      MIT License
      •1•5•0•0•Updated Feb 7, 2024Feb 7, 2024

    • qdnaseq

      Public
      A Nextflow pipeline to create qDNAseq bin annotations
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Sep 7, 2023Sep 7, 2023