CI connecting vg_construct_and_index and vg_multicall

[mlin]

The tests for vg_construct_and_index on the ABO locus example should proceed to run multi-caller workflow (2 mappers x 2 variant callers).

It needs GBWT index, which current ABOlocus/vg_construct_and_index doesn't yet build. We will have to add this and feed it 1000G phased haplotypes.

Documentation: https://github.com/vgteam/vg/wiki/Index-Construction#indexing-a-large-graph

[mlin]

Accessory issue: vg_construct_and_index is WDL 1.0, multicall is draft-2. Are there Cromwell issues blocking upgrading to WDL 1.0?

[mlin]

GBWT notes:

1. set vg construct -a, consuming VCF
2. set vg ids -m to get node mapping
3. GBWT indexing is its own little workflow: https://github.com/vgteam/vg/wiki/Index-Construction#with-haplotypes-3 in: vg, vcf.gz out: gbwt, threads
4. xg: consumes 'threads' outputs of GBWT indexing
5. prune: different invocation, consumes node mapping and gbwt files; becomes sequential instead of scattered
6. gcsa: consumes node mapping

Should we make this a second workflow, or pile everything into conditional features of the existing one?

VCF can become extremely large, and desirable to split by chr.

[mlin]

tentative plan: one workflow conditionally branching, and two different test invocations:

1. the deletion SV, no haplotypes.
2. small variants, with 1000G haplotypes

extract the small variants from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr9.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz