Lightning

Create a CWL pipeline to convert a VCF file with an associated BED file of homozygous reference regions to a gVCF file. The short term goal of the gVCF is to be fed into a Lightning pipeline for conversion to FastJ and ultimately Compact Genome Format (CGF).

There is preliminary work on doing this conversion with the command line tool vcfbed2homref. From a high level perspective, the CWL pipeline should just be a wrapper around this tool. Practically, there are some issues to work out, such as whether the input VCF is formatted properly (one large VCF file or multiple VCF files split by chromosome?) and making sure the resulting VCF file is indexed properly.

Part of the resolution of this ticket will be understanding what the expectations on input VCF + BED files are as well as understanding what the output requirements of the resulting gVCF files are.