TSPS-789 lower allowable nubmer of variants qc check to 3

[jsotobroad]

Description

We've noticed some submissions of WGS data to teaspoons' array imputation pipeline with just under 10 milliion variant sites. We dont want to allow that so are going to be stricter with the number of variants we allow. This should not affect actual array inputs.

https://broadworkbench.atlassian.net/browse/TSPS-789

Expected failure from the qc tests - https://app.terra.bio/#workspaces/warp-pipelines/WARP%20Tests/submission_history/2bd9ffba-29ee-4994-ac15-68b19802b759

2026-02-04 13:37:00.327 EST
< qc_messages Greater than 3 million variants found in the input VCF.
2026-02-04 13:37:00.327 EST
---
2026-02-04 13:37:00.327 EST
> qc_messages Greater than 10 million variants found in the input VCF.

We now log the number of variants in the input vcf for passing files. can be seen in https://app.terra.bio/#workspaces/warp-pipelines/WARP%20Tests/submission_history/67ff5012-8057-4537-81e8-a6f2b567a37c

2026-02-04 13:26:57.696 EST
1900151 variants found in input VCF.

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Checklist

If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP team by tagging @broadinstitute/warp-admins in a comment on this PR.

• Did you add inputs, outputs, or tasks to a workflow?
• Did you modify, delete or move: file paths, file names, input names, output names, or task names?
• If you made a changelog update, did you update the pipeline version number?

[github-actions]

Remember to squash merge!

[github-actions]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

[github-actions]

Remember to squash merge!

[github-actions]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

[mmorgantaylor]

Suggested change

	* Update input_qc_version to 1.2.5 to match the latest changes in InputQC wdl.
	* Update input_qc_version to 1.3.0 to match the latest changes in InputQC wdl.

[jsotobroad]

whoops, thanks!

[github-actions]

Remember to squash merge!

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

[github-actions]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.