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@biowdl

BioWDL

Bioinformatics workflows and tasks, written in WDL.

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  1. tasks tasks Public

    A collection of reusable WDL tasks. Category:Other

    WDL 85 29

  2. RNA-seq RNA-seq Public

    A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample

    WDL 31 17

  3. germline-DNA germline-DNA Public

    A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

    WDL 24 6

  4. wdl-packager wdl-packager Public

    Package a WDL and its imports into a zip file

    Python 8 2

  5. wdl-aid wdl-aid Public

    Automatic Input Documentation for WDL workflows

    Python 11 3

  6. ngs-performance-choices ngs-performance-choices Public

    Which tools to choose based on various performance metrics.

    7

Repositories

Showing 10 of 73 repositories
  • long-read-variant-calling Public

    Long read variant calling pipeline

    biowdl/long-read-variant-calling’s past year of commit activity
    WDL 0 MIT 0 0 1 Updated Dec 18, 2024
  • tasks Public

    A collection of reusable WDL tasks. Category:Other

    biowdl/tasks’s past year of commit activity
    WDL 85 MIT 29 1 1 Updated Dec 17, 2024
  • clinical-validation Public

    Check if a VCF for a benchmark sample matches the given output.

    biowdl/clinical-validation’s past year of commit activity
    WDL 1 MIT 0 0 2 Updated Nov 19, 2024
  • wdl-aid Public

    Automatic Input Documentation for WDL workflows

    biowdl/wdl-aid’s past year of commit activity
    Python 11 MIT 3 1 0 Updated Sep 5, 2024
  • WGSinCancerDiagnostics Public
    biowdl/WGSinCancerDiagnostics’s past year of commit activity
    WDL 7 MIT 0 0 0 Updated Jun 6, 2024
  • nanopore-sv Public

    A pipeline for Oxford nanopore ont structural variant calling

    biowdl/nanopore-sv’s past year of commit activity
    0 MIT 0 0 0 Updated Feb 13, 2024
  • germline-DNA Public

    A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

    biowdl/germline-DNA’s past year of commit activity
    WDL 24 MIT 6 1 1 Updated May 4, 2023
  • structural-variantcalling Public

    A workflow for calling structural variants. Category:Single-Sample

    biowdl/structural-variantcalling’s past year of commit activity
    WDL 8 MIT 3 0 0 Updated May 2, 2023
  • gatk-variantcalling Public

    A pipeline that calls variants on a group of BAM files. Category:Multi-Sample

    biowdl/gatk-variantcalling’s past year of commit activity
    WDL 2 MIT 3 0 0 Updated May 2, 2023
  • QC Public

    A BioWDL workflow for gathering QC metrics on and prepocessing FASTQ files. Category:Single-Sample

    biowdl/QC’s past year of commit activity
    WDL 2 MIT 2 2 0 Updated May 1, 2023
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