Choose sensible max alts default for PGEN extract [VS-1279] (#8811)

scripts/variantstore/docs/aou/AOU_DELIVERABLES.md

@@ -89,6 +89,7 @@
         - The `enable_extract_table_ttl` input should be set to `true` (the default value is `false`), which will add a TTL of two weeks to the tables it creates.
         - `extract_table_prefix` should be set to a name that is unique to the given Region / interval list. See the [naming conventions doc](https://docs.google.com/document/d/1pNtuv7uDoiOFPbwe4zx5sAGH7MyxwKqXkyrpNmBxeow) for guidance on what to use.
         - Specify the `interval_list` appropriate for the PGEN / VCF extraction run you are performing.
+        - `GvsExtractCallsetPgen` currently defaults to 100 alt alleles maximum, which means that any sites having more than that number of alt alleles will be dropped.
         - This workflow does not use the Terra Data Entity Model to run, so be sure to select the `Run workflow with inputs defined by file paths` workflow submission option.
     - Specify the same `call_set_identifier`, `dataset_name`, `project_id`, `extract_table_prefix`, and `interval_list` that were used in the `GvsPrepareRangesCallset` run documented above.
     - Specify the `interval_weights_bed` appropriate for the PGEN / VCF extraction run you are performing. `gs://gvs_quickstart_storage/weights/gvs_full_vet_weights_1kb_padded_orig.bed` is the interval weights BED used for Quickstart.

scripts/variantstore/wdl/GvsExtractCallsetPgen.wdl

@@ -16,8 +16,10 @@ workflow GvsExtractCallsetPgen {
         # reference (see plink chromosome codes here: https://www.cog-genomics.org/plink/2.0/data#irreg_output)
         # ExtractCohortToPgen currently only supports codes "chrM" and "MT"
         String pgen_chromosome_code = "chrM"
-        # Max number of alt alleles a site can have. If a site exceeds this number, it will not be written (max 254)
-        Int max_alt_alleles = 254
+        # Max number of alt alleles a site can have. If a site exceeds this number, it will not be written (max 254).
+        # PGEN extract is currently only used for AoU "small callsets" which always want 100 max alt alleles, so default
+        # to that value.
+        Int max_alt_alleles = 100
         # If true, does not throw an exception for samples@sites with unsupported ploidy (codes it as missing instead)
         Boolean lenient_ploidy_validation = false
         # If true, preserves phasing in the output PGEN files if phasing is present in the source genotypes
@@ -318,7 +320,7 @@ task PgenExtractTask {
         # ExtractCohortToPgen currently only supports codes "chrM" and "MT"
         String pgen_chromosome_code
         # Max number of alt alleles a site can have. If a site exceeds this number, it will not be written (max 254)
-        Int? max_alt_alleles
+        Int max_alt_alleles
         # If true, does not throw an exception for samples@sites with unsupported ploidy (codes it as missing instead)
         Boolean? lenient_ploidy_validation
         # If true, preserves phasing in the output PGEN files if phasing is present in the source genotypes