BioWDL

All

73 repositories

long-read-variant-calling
Public
Long read variant calling pipeline
WDL
•
MIT License
•0•0•0•1•Updated Dec 18, 2024Dec 18, 2024
tasks
Public
A collection of reusable WDL tasks. Category:Other
workflow bioinformatics tasks bioinformatics-pipeline wdl wdl-tasks
WDL
•
MIT License
•29•85•1•1•Updated Dec 17, 2024Dec 17, 2024
clinical-validation
Public
Check if a VCF for a benchmark sample matches the given output.
WDL
•
MIT License
•0•1•0•2•Updated Nov 19, 2024Nov 19, 2024
wdl-aid
Public
Automatic Input Documentation for WDL workflows
documentation jinja2 documentation-generator wdl wdl-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
pipeline somatic-variants wdl structural-variation germline-variants variantcalling multisample gatk4 gatk-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
workflow bioinformatics variant-calling gatk4 gatk-bestpractices workflows
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
bioinformatics quality-control pipeline next-generation-sequencing bioinformatics-pipeline wdl fastq workflow
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
pipeline wdl bam
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
wdl multisample gatk4 gatk-bestpractices rna-seq pipeline
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.
pipeline wdl chip-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
pipeline wdl variantcalling
WDL
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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
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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.
bioinformatics reproducible test test-data reusable bioinformatics-data biowdl
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