It is impossible to use SAMtools out of the sample "Call variants with SAMtools"

The workflow element "Call Variants with SAMtools" is used in the sample with the same name. This sample is developed to be handy (with a wizard), it can process a lot of input datasets.

But it is hard to use it (or even impossible) in a workflow: Aligner (BWA) -> Call variants.

1. References. There are 2 input ports, and 1 of them is a reference port. But when you align with BWA different datasets of reads, the corresponding BWA element gets only 1 reference (as a parameter). This mismatch in references count doesn't let to use that workflow correctly.
2. Datasets. BWA doesn't produce datasets (actually, it is a BWA bug). So, "Call variants with SAMtools" can't produce several output VCFs.

A possible solution here is to create a parameter for reference input type: from a file or form a port. This parameter changes the number of ports in the element.