Undefined output_ vcf when using vcfeval

I am running the command using Nextflow:

/opt/hap.py/bin/hap.py \\
      $truth $filtered \\
      -f $cr_bed \\
      -o happy_annotated \\
      -r $reference \\
      --engine=vcfeval \\
      --engine-vcfeval-template $sdf \\
      -V \\
      --preserve-info \\
      --threads $task.cpus

Which leads to the following error:

  2020-01-23 23:59:38,511 ERROR    global name 'output_vcf' is not defined
  2020-01-23 23:59:38,511 ERROR    Traceback (most recent call last):
  2020-01-23 23:59:38,511 ERROR      File "/opt/hap.py/bin/hap.py", line 508, in <module>
  2020-01-23 23:59:38,511 ERROR        main()
  2020-01-23 23:59:38,511 ERROR      File "/opt/hap.py/bin/hap.py", line 485, in main
  2020-01-23 23:59:38,512 ERROR        bcftools.runBcftools("merge", output_vcf, info_file.name,
  2020-01-23 23:59:38,512 ERROR    NameError: global name 'output_vcf' is not defined

Which points to the following line in hap.py:

bcftools.runBcftools("merge", output_vcf, info_file.name,
                        "-m", "all",
                        "|", "bcftools", "view", "-s", "^TRUTH_IN,QUERY_IN", "-X", "-U",
                        "-o", merged_info_file.name, "-O", "z")

This is the only place that ouput_vcf appears in hap.py thus I assume it was missed when a variable name was changed.

I will re-run without vcfeval but I would prefer to use it.

Illumina / hap.py

Undefined output_ vcf when using vcfeval #105