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@biowdl

BioWDL

Bioinformatics workflows and tasks, written in WDL.

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  1. tasks Public

    A collection of reusable WDL tasks. Category:Other

    WDL 86 30

  2. 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 18

  3. germline-DNA Public

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

    WDL 26 7

  4. wdl-packager Public

    Package a WDL and its imports into a zip file

    Python 7 2

  5. wdl-aid Public

    Automatic Input Documentation for WDL workflows

    Python 12 3

  6. ngs-performance-choices Public

    Which tools to choose based on various performance metrics.

    8

Repositories

Showing 10 of 73 repositories
  • tasks Public

    A collection of reusable WDL tasks. Category:Other

    WDL 86 MIT 30 1 1 Updated Mar 21, 2025
  • long-read-variant-calling Public

    Long read variant calling pipeline

    WDL 0 MIT 0 0 0 Updated Mar 12, 2025
  • clinical-validation Public

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

    WDL 1 MIT 0 0 1 Updated Mar 12, 2025
  • wdl-aid Public

    Automatic Input Documentation for WDL workflows

    Python 12 MIT 3 1 0 Updated Sep 5, 2024
  • WDL 7 MIT 0 0 0 Updated Jun 6, 2024
  • nanopore-sv Public

    A pipeline for Oxford nanopore ont structural variant calling

    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

    WDL 26 MIT 7 1 1 Updated May 4, 2023
  • structural-variantcalling Public

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

    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

    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

    WDL 2 MIT 2 2 0 Updated May 1, 2023