Janis - Example Pipelines
This repository contains workflows written using Janis.
These workflows are installed by default, but are available on PIP with:
pip3 install janis-pipelines.pipelinesDocumentation
These pipelines are documented with run instructions here: https://janis.readthedocs.io/en/latest/pipelines/index.html
More information
These pipelines are made available through the entrypoint: janis.extension=pipelines.
They can be imported in Python with the following:
from janis_pipelines import WGSGermlineGATK
WGSGermlineGATK().translate("wdl")Pipelines
Whole genome sequencing (WGS) pipelines:
Other:
Reference files:
- Tested with
hg38from GCS: Broad Institute
WGS Germline pipeline
See the - germline folder for more information, the workflow and CWL / WDL translations.
The WGS germline pipeline takes a FASTQ pair, aligns, sorts, marks duplicates and calls variants across GATK4, Strelka and VarDict. These variants are combined and sorted at the end.
These variants were validated against the Genome in a Bottle data sets to achieve:
- Recall: 99.25%
- Precision: 92.02%
These results were identical across 3 research institutes (combination of Slurm / PBS / Torque) and Google Cloud platform. The pipeline took approximately 27-30 hours to run at a 30x coverage, depending on the resource constraint.
WGS Somatic pipeline for tumor-normal variant discovery
See the somatic folder for more information, the workflow and CWL / WDL translations.
The WGS somatic pipeline takes normal and tumor FASTQ pairs, aligns, sorts and marks duplicates separately, and then performs tumor-normal variant discovery across GATK4, Strelka and VarDict (in somatic modes). These variants are combined and sorted at the end.
This pipeline was run successfully across a similar set of research institutes (as germline) and the cloud, however these variants have not been validated yet.
