Repositories list

• long-read-variant-calling

  Public
  Long read variant calling pipeline

  WDL

  •

  MIT License

  •0•0•0•0•Updated Nov 11, 2024Nov 11, 2024

• tasks

  Public
  A collection of reusable WDL tasks. Category:Other

  workflowbioinformaticstasks+ 3bioinformatics-pipelinewdlwdl-tasks

  WDL

  •

  MIT License

  •31•85•1•0•Updated Nov 11, 2024Nov 11, 2024

• clinical-validation

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

  WDL

  •

  MIT License

  •0•1•0•1•Updated Oct 18, 2024Oct 18, 2024

• wdl-aid

  Public
  Automatic Input Documentation for WDL workflows

  documentationjinja2documentation-generator+ 2wdlwdl-workflows

  Python

  •

  MIT License

  •3•11•1•0•Updated Sep 5, 2024Sep 5, 2024

• WGSinCancerDiagnostics

  Public
  WDL

  •

  MIT License

  •0•7•0•0•Updated Jun 6, 2024Jun 6, 2024

• nanopore-sv

  Public
  A pipeline for Oxford nanopore ont structural variant calling

  MIT License

  •0•0•0•0•Updated Feb 13, 2024Feb 13, 2024

• germline-DNA

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

  pipelinesomatic-variantswdl+ 6structural-variationgermline-variantsvariantcallingmultisamplegatk4gatk-bestpractices

  WDL

  •

  MIT License

  •6•24•1•1•Updated May 4, 2023May 4, 2023

• structural-variantcalling

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

  WDL

  •

  MIT License

  •3•8•0•0•Updated May 2, 2023May 2, 2023

• gatk-variantcalling

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

  workflowbioinformaticsvariant-calling+ 3gatk4gatk-bestpracticesworkflows

  WDL

  •

  MIT License

  •3•2•0•0•Updated May 2, 2023May 2, 2023

• QC

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

  bioinformaticsquality-controlpipeline+ 5next-generation-sequencingbioinformatics-pipelinewdlfastqworkflow

  WDL

  •

  MIT License

  •2•2•2•0•Updated May 1, 2023May 1, 2023

• gatk-CNVcalling

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

  WDL

  •

  MIT License

  •0•0•0•1•Updated May 1, 2023May 1, 2023

• BamMetrics

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

  pipelinewdlbam

  WDL

  •

  MIT License

  •6•0•0•0•Updated Apr 28, 2023Apr 28, 2023

• scripts

  Public
  Scripts for releasing, updating docs etc. in biowdl repos

  Shell

  •

  MIT License

  •2•1•1•0•Updated Apr 28, 2023Apr 28, 2023

• RNA-seq

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

  wdlmultisamplegatk4+ 3gatk-bestpracticesrna-seqpipeline

  WDL

  •

  MIT License

  •17•31•4•0•Updated Mar 10, 2023Mar 10, 2023

• docker-cuppa

  Public
  A docker image for hartwigmedical/hmftools' CUPPA.

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 21, 2023Feb 21, 2023

• docker-peach

  Public
  A docker image for hartwigmedical's PEACH.

  Dockerfile

  •0•0•0•0•Updated Feb 21, 2023Feb 21, 2023

• docker-gridss

  Public
  Dockerfile

  •0•0•0•0•Updated Feb 17, 2023Feb 17, 2023

• ChIP-seq

  Public
  A BioWDL pipeline for processing ChIP-seq data.

  pipelinewdlchip-seq

  WDL

  •1•0•0•0•Updated Jan 27, 2023Jan 27, 2023

• uniparental-disomy

  Public
  A simple pipeline to find uniparental-disomy based on GVCF data using UPDio

  MIT License

  •0•1•0•1•Updated Dec 21, 2022Dec 21, 2022

• wdl-packager

  Public
  Package a WDL and its imports into a zip file

  Python

  •

  MIT License

  •2•8•1•0•Updated Oct 31, 2022Oct 31, 2022

• somatic-variantcalling

  Public
  A pipeline for somatic variantcalling. Category:Single-Sample

  pipelinewdlvariantcalling

  WDL

  •

  MIT License

  •1•8•0•0•Updated Aug 22, 2022Aug 22, 2022

• docker-linx

  Public
  A docker image containing the Hartwig Medical Foundation's linx.

  Dockerfile

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 5, 2022Aug 5, 2022

• docker-health-checker

  Public
  A docker image containing the Hartwig Medical Foundation's health-checker

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 5, 2022Aug 5, 2022

• biotdg

  Public
  Bioinformatics Test Data Generator

  Python

  •

  MIT License

  •0•1•0•0•Updated Jun 24, 2022Jun 24, 2022

• biowdl-test-data

  Public
  Reproducible and reusable test data for bioinformatics projects.

  bioinformaticsreproducibletest+ 4test-datareusablebioinformatics-databiowdl

  Python

  •

  MIT License

  •1•3•0•0•Updated Jun 20, 2022Jun 20, 2022

• docker-orange

  Public
  A docker image for hartwigmedical/hmftools' orange.

  Python

  •0•0•0•0•Updated Mar 2, 2022Mar 2, 2022

• docker-virus-interpreter

  Public
  A docker image for hartwigmedical/hmftools' virus-interpreter

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 25, 2022Feb 25, 2022

• gatk-preprocess

  Public
  A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. Category:Single-Sample

  pipeline

  WDL

  •

  MIT License

  •3•2•0•0•Updated Feb 15, 2022Feb 15, 2022

• docker-protect

  Public
  A docker image for hartwigmedical/hmftools' protect

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 11, 2022Feb 11, 2022

• docker-pave

  Public
  A docker image for hartwigmedical/hmftools' pave

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 10, 2022Feb 10, 2022