/**
* Perform filtering on all VCF files for a given workflow. Filtering involves removing lines that
* are not "PASS" or "." Output files will have ".pass-filtered." in their name.
*
* @param workflowName The workflow to PASS filter
* @param parents List of parent jobs.
* @return
*/
private Job passFilterWorkflow(Pipeline workflowName, Job... parents) {
// Job passFilter = this.getWorkflow().createBashJob("pass filter "+workflowName);
PreprocessJobGenerator generator =
new PreprocessJobGenerator(
this.JSONlocation, this.JSONrepoName, this.JSONfolderName, this.JSONfileName);
Job passFilter = generator.passFilterWorkflow(this, workflowName, parents);
return passFilter;
}
