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@biowdl

BioWDL

Bioinformatics workflows and tasks, written in WDL.

Pinned

  1. tasks tasks Public

    A collection of reusable WDL tasks. Category:Other

    WDL 84 31

  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 16

  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 23 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.

    6

Repositories

Showing 10 of 72 repositories
  • nanopore-sv Public

    A pipeline for Oxford nanopore ont structural variant calling

    0 MIT 0 0 0 Updated Feb 13, 2024
  • WDL 7 MIT 0 0 0 Updated Sep 29, 2023
  • tasks Public

    A collection of reusable WDL tasks. Category:Other

    WDL 84 MIT 31 1 0 Updated Sep 29, 2023
  • germline-DNA Public

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

    WDL 23 MIT 6 1 1 Updated May 4, 2023
  • structural-variantcalling Public

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

    WDL 8 MIT 4 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 1 2 0 Updated May 1, 2023
  • gatk-CNVcalling Public

    The BioWDL implemention of the GATK CNV calling workflow. Category:Multi-Sample

    WDL 0 MIT 0 0 1 Updated May 1, 2023
  • BamMetrics Public

    A BioWDL workflow for gathering metrics from a BAM file. Category:Single-Sample

    WDL 0 MIT 6 0 0 Updated Apr 28, 2023
  • scripts Public

    Scripts for releasing, updating docs etc. in biowdl repos

    Shell 1 MIT 2 1 0 Updated Apr 28, 2023

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