[Snyk] Security upgrade ubuntu from noble-20250925 to 24.04 #288
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The following vulnerabilities are fixed with an upgrade: - https://snyk.io/vuln/SNYK-UBUNTU2404-GNUPG2-14849555 - https://snyk.io/vuln/SNYK-UBUNTU2404-PAM-11936905 - https://snyk.io/vuln/SNYK-UBUNTU2404-PAM-11936905 - https://snyk.io/vuln/SNYK-UBUNTU2404-PAM-11936905 - https://snyk.io/vuln/SNYK-UBUNTU2404-PAM-11936905
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This is an update from a development build ( Source: Ubuntu release documentation
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The corresponding package.json needs to have the version updated. All references to the image also need to be bumped to the new version. |
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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: - [x] You have added a few sentences describing the PR here. - [x] The code passes all CI tests without any errors or warnings. - [x] You have added tests (when appropriate). - [x] You have added an entry in any relevant CHANGELOGs (when appropriate). - [x] If you have made any changes to the `scripts/` or `docker/` directories, please ensure any image versions have been incremented accordingly! - [x] You have updated the README or other documentation to account for these changes (when appropriate). <!-- START COPILOT CODING AGENT SUFFIX --> <!-- START COPILOT ORIGINAL PROMPT --> <details> <summary>Original prompt</summary> > Pull Request: #288 </details> <!-- START COPILOT CODING AGENT TIPS --> --- 💬 We'd love your input! Share your thoughts on Copilot coding agent in our [2 minute survey](https://gh.io/copilot-coding-agent-survey). --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: adthrasher <1165729+adthrasher@users.noreply.github.com>
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Snyk Container found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.
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Snyk has created this PR to fix 2 vulnerabilities in the dockerfile dependencies of this project.
Keeping your Docker base image up-to-date means you’ll benefit from security fixes in the latest version of your chosen image.
Snyk changed the following file(s):
docker/util/DockerfileWe recommend upgrading to
ubuntu:24.04, as this image has only 8 known vulnerabilities. To do this, merge this pull request, then verify your application still works as expected.Vulnerabilities that will be fixed with an upgrade:
SNYK-UBUNTU2404-GNUPG2-14849555
SNYK-UBUNTU2404-PAM-11936905
SNYK-UBUNTU2404-PAM-11936905
SNYK-UBUNTU2404-PAM-11936905
SNYK-UBUNTU2404-PAM-11936905
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