dax2dot -s -o test.dot test.dax

The dependency between jobs check::reads:1.0 and alignment::bowtie2_transcriptome:1.0 is correctly shown.
Note: The jobs depend on each other, but not based on the output file of the check::reads:1.0 job. It is logical; if the file check fails do not proceed.

dax2dot -s -f -o test.dot test.dax

There is no dependency represented between jobs check::reads:1.0 and alignment::bowtie2_transcriptome:1.0