A collection of WDL pipelines for sequencing analyses.


BioWDL is a collection of pipelines and workflows usable for a variety of sequencing related analyses. They are made using WDL and are developed at the Leiden University Medical Center by the SASC team.

Pipelines and other repositories

The following are the pipelines and repositories from BioWDL. The repositories are divided into the following categories:

Name Category Description
BamMetrics (repo) Single-Sample A BioWDL workflow for gathering metrics from a BAM file.
expression-quantification (repo) Multi-Sample A BioWDL workflow for quantifying expression.
gatk-CNVcalling (repo) Multi-Sample The BioWDL implemention of the GATK CNV calling workflow.
gatk-preprocess (repo) Single-Sample A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices.
gatk-variantcalling (repo) Multi-Sample A pipeline that calls variants on a group of BAM files.
germline-DNA (repo) Multi-Sample A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files.
QC (repo) Single-Sample A BioWDL workflow for gathering QC metrics on and prepocessing FASTQ files.
RNA-seq (repo) Multi-Sample A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs.
sequence-classification (repo) Single-Sample A workflow for processing metagenomics data sets using Centrifuge.
small-rna (repo) Multi-Sample Small rna pipeline.
somatic-variantcalling (repo) Single-Sample A pipeline for somatic variantcalling.
structural-variantcalling (repo) Single-Sample A workflow for calling structural variants.
TALON-WDL (repo) Multi-Sample InDevelopment WDL implementation of the TALON workflow.
tasks (repo) Other A collection of reusable WDL tasks.


Please feel free to make a pull requests if you have something you would like to add or improve. Below you can find a link to the style guidelines these pipelines should adhere to, as well as some notes on adding tests.

Style guidelines

You can find the style guidelines here. The BioWDL pipelines should adhere to these guidelines as much as possible. If something is unclear or you feel something is missing, please don’t hesitate to make an issue or pull request.

Functional tests

You can find documentation on the automated testing used in BioWDL here.


For any question related to any BioWDL workflows, please use the relevant github issue tracker or contact the SASC team directly at: