Pinned Repositories
germline-DNA
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
mkbigfifo
A script to make FIFO files (pipes) with the maximum allowed buffer size
ngs-performance-choices
Which tools to choose based on various performance metrics.
RNA-seq
A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample
somatic-variantcalling
A pipeline for somatic variantcalling. Category:Single-Sample
structural-variantcalling
A workflow for calling structural variants. Category:Single-Sample
tasks
A collection of reusable WDL tasks. Category:Other
wdl-aid
Automatic Input Documentation for WDL workflows
wdl-packager
Package a WDL and its imports into a zip file
WGSinCancerDiagnostics
BioWDL's Repositories
biowdl/tasks
A collection of reusable WDL tasks. Category:Other
biowdl/RNA-seq
A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample
biowdl/germline-DNA
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
biowdl/wdl-aid
Automatic Input Documentation for WDL workflows
biowdl/somatic-variantcalling
A pipeline for somatic variantcalling. Category:Single-Sample
biowdl/structural-variantcalling
A workflow for calling structural variants. Category:Single-Sample
biowdl/wdl-packager
Package a WDL and its imports into a zip file
biowdl/WGSinCancerDiagnostics
biowdl/biowdl-test-data
Reproducible and reusable test data for bioinformatics projects.
biowdl/gatk-preprocess
A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. Category:Single-Sample
biowdl/gatk-variantcalling
A pipeline that calls variants on a group of BAM files. Category:Multi-Sample
biowdl/QC
A BioWDL workflow for gathering QC metrics on and prepocessing FASTQ files. Category:Single-Sample
biowdl/biotdg
Bioinformatics Test Data Generator
biowdl/clinical-validation
Check if a VCF for a benchmark sample matches the given output.
biowdl/expression-quantification
A BioWDL workflow for quantifying expression. Category:Multi-Sample
biowdl/scripts
Scripts for releasing, updating docs etc. in biowdl repos
biowdl/uniparental-disomy
A simple pipeline to find uniparental-disomy based on GVCF data using UPDio
biowdl/BamMetrics
A BioWDL workflow for gathering metrics from a BAM file. Category:Single-Sample
biowdl/ChIP-seq
A BioWDL pipeline for processing ChIP-seq data.
biowdl/docker-cuppa
A docker image for hartwigmedical/hmftools' CUPPA.
biowdl/docker-gridss
biowdl/docker-health-checker
A docker image containing the Hartwig Medical Foundation's health-checker
biowdl/docker-linx
A docker image containing the Hartwig Medical Foundation's linx.
biowdl/docker-orange
A docker image for hartwigmedical/hmftools' orange.
biowdl/docker-pave
A docker image for hartwigmedical/hmftools' pave
biowdl/docker-peach
A docker image for hartwigmedical's PEACH.
biowdl/docker-protect
A docker image for hartwigmedical/hmftools' protect
biowdl/docker-virus-interpreter
A docker image for hartwigmedical/hmftools' virus-interpreter
biowdl/gatk-CNVcalling
The BioWDL implemention of the GATK CNV calling workflow. Category:Multi-Sample
biowdl/nanopore-sv
A pipeline for Oxford nanopore ont structural variant calling