TSPS-342 Update reheader seq dict wdl for better efficiency

[mmorgantaylor]

Description

Make reheadering of VCFs with correct sequence dictionary more efficient, since we'll need to run it on the AoU+AnVIL reference panel VCFs and that will take a long time.

Changes:

• extract the header, fix it, then reheader the original, rather than fixing it in the original in one step
• use bcftools to create index instead of tabix
• add echos with dates for better progress tracking

Some learnings about timing:

• the vast majority of this task is spent creating the index
• next longest step is localization of the files (1 hour for chr20 vcf)

Note we ran this with a monitoring script and found that the task was not close to using all the memory available (memory utilization did not exceed 11%), so we don't think an optimization there would help. We also weren't pegged on iops (didn't exceed 40 MiB/s, and the max on the machine is >200 MiB/s).

Evaluation:
Before these changes, this wdl run on the AoU-only chr20 vcf took 29+ hours, cost $2.37.
After these changes, the same input took 23 hours (20% improvement), cost $1.87 (21% improvement).

Jira Ticket

https://broadworkbench.atlassian.net/browse/TSPS-342

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud