This may be unhelpful, but have you tried pulling a different version of heudiconv?
I created my singularity image using singularity pull docker://nipy/heudiconv:0.5.4 (we have singularity 3 installed on our cluster), but also have it working with the debian heudiconv release: https://hub.docker.com/r/nipy/heudiconv/tags
See however my issue at: Overwriting heudiconv sub.auto.txt and sub.edit.txt