Batch launching workflows with multiple inputs

This section describes the launching of workflows with multiple inputs, where all input elements will be changed per batch. This launch mechanism is not intended for workflows with multiple input elements where one of the input elements remains the same in all batches, such as workflows meant to compare several tissues to a unique control tissue. At the moment, batch launching of such workflows is not possible, unless the common item is saved under different names as many times as there should be batches.

For workflows with multiple inputs where the inputs all need to change for each batch run, information specifying the grouping of the data elements and what role each element plays in a given analysis needs to be imported into the system from an Excel spreadsheet.

The requirements for launching such workflows in batch mode are:

Ready-to-use workflows with more than one input in the Biomedical Genomics Workbench fall within two categories; 1) the Somatic Cancer workflow that compares tumor and normal samples, and 2) the Hereditary Disease workflows where a trio or a family of four is analyzed in one workflow.

(Figure 7.8) shows an example of the spreadsheet used in the Somatic Cancer workflows.

Image spreadsheet_batching
Figure 7.8: Example of a spreadhseet necessary to run a workflow in batch, where the workflow intend to compare two samples.

To launch a workflow with multiple input elements in batch mode:

Important note: When running the Identify Rare Disease Causing Mutations ready-to-use workflows in batch mode, the gender of all proband samples in a given batch run must be the same. In other words, if multiple families are analyzed in a batch run, the probands must all be female or they must all be male. This is because proband gender is specified as a parameter, and the parameter values provided when setting up a workflow are then used for each analysis in the batch. The same condition applies when running a workflow in batch mode that includes a Trio Analysis. The gender of all child samples being analyzed in a given batch run must be the same.