Bump util Docker image version for Ubuntu 24.04 base upgrade

[Copilot]

Completes Snyk PR #288 which upgraded the util Dockerfile base image from ubuntu:noble-20250925 to ubuntu:24.04 (fixes CVE-2024-53055 and CVE-2024-53924). The Dockerfile change alone would fail CI validation - container version tags must match package.json and all WDL workflow references must use the current version.

Changes

• Bumped docker/util/package.json version: 3.0.1 → 3.0.2
• Updated 16 container references across 9 WDL files to use ghcr.io/stjudecloud/util:3.0.2

Affected Files

Config:

• docker/util/package.json

Workflows using util container:

• data_structures/flag_filter.wdl
• data_structures/read_group.wdl (3 references)
• tools/htseq.wdl
• tools/md5sum.wdl
• tools/util.wdl (7 references)
• workflows/dnaseq/dnaseq-standard.wdl
• workflows/qc/quality-check-standard.wdl
• workflows/rnaseq/rnaseq-standard.wdl

Before submitting this PR, please make sure:

• You have added a few sentences describing the PR here.
• The code passes all CI tests without any errors or warnings.
• You have added tests (when appropriate).
• You have added an entry in any relevant CHANGELOGs (when appropriate).
• If you have made any changes to the scripts/ or docker/ directories, please ensure any image versions have been incremented accordingly!
• You have updated the README or other documentation to account for these changes (when appropriate).

Original prompt

Pull Request: #288

---

💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.