Parliament2 never terminates if running CNVnator with svtyper

[tfenne]

I'm running P2 with a command line that includes --cnvnator --genotype, using the latest docker image as of today. The job never terminates, but instead is left sitting with a single process running which is python /get_uncalled_cnvnator.py.

The problem occurs here: https://github.com/dnanexus/parliament2/blob/master/parliament2.sh#L469

The offending code is:
python /get_uncalled_cnvnator.py | python /add_ciend.py 1000 > cnvnator.ci.vcf < cnvnator.vcf

The problem is that the input redirect is attached to the second process, not the first. Thus add-ciend.py runs on the input VCF and generates the output VCF with all cnvnator calls and get_uncalled_cnvnator.py just sits there waiting for someone to write to it's stdin.