The ploidy estimation script uses string comparison to "X" and "Y" to
identify sex chromsomes, but the ploidy matrix input to the script uses
"chrX" and "chrY" for the sex chromsomes. This commit updates the script
to correctly identify sex chrosomomes.

Update the ploidy estimation script and associated WDLs to accept a
custom set of allosome contigs, with the default being chrX and chrY.

Expose separate inputs to specify the allosomal contig names in
PloidyEstimation with the defaults being "chrX" and "chrY".

The method to pass the names of the allosomes to PloidyEstimation was
changed from passing a file to passing two strings, but some calling
workflows were not updated to reflect the change. This commit fixes the
inputs.