Fix tests

See merge request !5

This is done to work around a bug in the latest version of
pytest-workflow, https://github.com/LUMC/pytest-workflow/issues/122

Sending the coverage data to varda was run as a local rule, which caused
the SGE cluster to kill the wrapper script when there were many samples.

This commit removes the local rule so that the jobs to submit the data
to varda are submitted to the cluster as well.

Resolve "Disease code can be "\n""

Closes #1

See merge request !4

Use latest version of varda2-client.

See merge request !3

Add testing to vcf-to-varda

See merge request !2

van den Berg authored 4 years ago and Santcroos committed 4 years ago

The first step of the pipeline is to use bcftools to filter alt alleles
that are not present in any of the called genotypes, and to remove the
alt alleles of genotypes that are uncalled.