BioWDL's repositories
germline-DNA
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
somatic-variantcalling
A pipeline for somatic variantcalling. Category:Single-Sample
structural-variantcalling
A workflow for calling structural variants. Category:Single-Sample
wdl-packager
Package a WDL and its imports into a zip file
biowdl-test-data
Reproducible and reusable test data for bioinformatics projects.
gatk-preprocess
A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. Category:Single-Sample
gatk-variantcalling
A pipeline that calls variants on a group of BAM files. Category:Multi-Sample
clinical-validation
Check if a VCF for a benchmark sample matches the given output.
expression-quantification
A BioWDL workflow for quantifying expression. Category:Multi-Sample
uniparental-disomy
A simple pipeline to find uniparental-disomy based on GVCF data using UPDio
BamMetrics
A BioWDL workflow for gathering metrics from a BAM file. Category:Single-Sample
ChIP-seq
A BioWDL pipeline for processing ChIP-seq data.
docker-cuppa
A docker image for hartwigmedical/hmftools' CUPPA.
docker-health-checker
A docker image containing the Hartwig Medical Foundation's health-checker
docker-linx
A docker image containing the Hartwig Medical Foundation's linx.
docker-orange
A docker image for hartwigmedical/hmftools' orange.
docker-pave
A docker image for hartwigmedical/hmftools' pave
docker-peach
A docker image for hartwigmedical's PEACH.
docker-protect
A docker image for hartwigmedical/hmftools' protect
docker-virus-interpreter
A docker image for hartwigmedical/hmftools' virus-interpreter
gatk-CNVcalling
The BioWDL implemention of the GATK CNV calling workflow. Category:Multi-Sample
nanopore-sv
A pipeline for Oxford nanopore ont structural variant calling