SnpEff annotation step: `vcf_snpeff_annotation.py` script fails with EOFError

[kamyshova]

Background

In SnpEff annotation workflow step, a src/python/vcf_snpeff_annotation.py script is used to annotate the consequence of the variants. If the input VCF file doesn’t have a ‘PASS’ variants the vcf_snpeff_annotation.py script fails with EOFError (input VCF file is empty). Although this error doesn't affect the overall execution of the workflow, the error output file will contain this error.

Approach

It might be worthwhile to anticipate this behavior and add validation to the script.