feat: support task.ext.args in sentieon/gvcftyper

[nicorap]

Description

Add task.ext.args support to SENTIEON_GVCFTYPER, matching the convention already used by sibling sentieon modules (haplotyper, varcal, applyvarcal,
dnascope, applyvarcal, etc.).

+ def args = task.ext.args ?: ''
  ...
  sentieon driver \
      -r ${fasta} \
      ${interval_command} \
      --algo GVCFtyper \
+     ${args} \
      ${gvcfs_input} \
      ${dbsnp_cmd} \
      ${prefix}.vcf.gz

${args} is injected after --algo GVCFtyper, so callers pass algorithm-level options (--emit_mode, --call_conf,
--allow-old-rms-mapping-quality-annotation-data, etc.). Driver-level flags (-t, --interval) remain managed by the module since they relate to inputs the
module already owns.

Reason for PR

nf-core/sarek's joint-germline path needs to call GVCFtyper in two distinct modes for very large cohorts:

• SHARD (per interval, per sample-batch): --emit_mode all_samples to produce batch-aggregated intermediates
• REDUCE (per interval, over batch intermediates): default emit mode for the final joint VCF

Without ext.args support, sarek currently has to ship a local fork of the module (modules/local/sentieon/gvcftyper/) that's identical to the upstream module
except for these two lines. This PR removes that need.

Tests

No new tests added — the change is a no-op when task.ext.args is unset (the default), which is what every existing test exercises. They continue to pass
unchanged.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests! — existing tests cover the empty-args path; non-empty args is pass-through
• If you've added a new tool - have you followed the module conventions in the contribution
  docs — N/A, existing module
• If necessary, include test data in your PR. — no new data
• Remove all TODO statements.
• Broadcast software version numbers to topic: versions — unchanged
• Follow the naming conventions. — unchanged
• Follow the parameters requirements. — unchanged
• Follow the input/output options guidelines. — unchanged
• Add a resource label — label 'process_high' already present
• Use BioConda and BioContainers if possible to fulfil software requirements. — already configured
• For modules:
  • nf-core modules test sentieon/gvcftyper --profile docker
  • nf-core modules test sentieon/gvcftyper --profile singularity
  • nf-core modules test sentieon/gvcftyper --profile conda

Relying on the CI matrix (license-server credentials only available from upstream branches).

[SPPearce]

The GitHub actions seem to be down at the moment

[asp8200]

I see this thing with the --emit_mode was handled a bit differently in the other sentieon modules, for instance, here.

Over in Sarek, we then have the option --sentieon_haplotyper_emit_mode.