chore(Snyk): Security upgrade ubuntu from noble-20250925 to noble-20260113 (#288)

![snyk-top-banner](https://res.cloudinary.com/snyk/image/upload/r-d/scm-platform/snyk-pull-requests/pr-banner-default.svg)

### 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/Dockerfile`

We 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:

|  | Issue | Score | 

:-------------------------:|:-------------------------|:-------------------------
![high
severity](https://res.cloudinary.com/snyk/image/upload/w_20,h_20/v1561977819/icon/h.png
'high severity') | Out-of-bounds Write
<br/>[SNYK-UBUNTU2404-GNUPG2-14849555](https://snyk.io/vuln/SNYK-UBUNTU2404-GNUPG2-14849555)
| &nbsp;&nbsp;**281**&nbsp;&nbsp;
![medium
severity](https://res.cloudinary.com/snyk/image/upload/w_20,h_20/v1561977819/icon/m.png
'medium severity') | Directory Traversal
<br/>[SNYK-UBUNTU2404-PAM-11936905](https://snyk.io/vuln/SNYK-UBUNTU2404-PAM-11936905)
| &nbsp;&nbsp;**231**&nbsp;&nbsp;
![medium
severity](https://res.cloudinary.com/snyk/image/upload/w_20,h_20/v1561977819/icon/m.png
'medium severity') | Directory Traversal
<br/>[SNYK-UBUNTU2404-PAM-11936905](https://snyk.io/vuln/SNYK-UBUNTU2404-PAM-11936905)
| &nbsp;&nbsp;**231**&nbsp;&nbsp;
![medium
severity](https://res.cloudinary.com/snyk/image/upload/w_20,h_20/v1561977819/icon/m.png
'medium severity') | Directory Traversal
<br/>[SNYK-UBUNTU2404-PAM-11936905](https://snyk.io/vuln/SNYK-UBUNTU2404-PAM-11936905)
| &nbsp;&nbsp;**231**&nbsp;&nbsp;
![medium
severity](https://res.cloudinary.com/snyk/image/upload/w_20,h_20/v1561977819/icon/m.png
'medium severity') | Directory Traversal
<br/>[SNYK-UBUNTU2404-PAM-11936905](https://snyk.io/vuln/SNYK-UBUNTU2404-PAM-11936905)
| &nbsp;&nbsp;**231**&nbsp;&nbsp;



---

> [!IMPORTANT]
>
> - Check the changes in this PR to ensure they won't cause issues with
your project.
> - Max score is 1000. Note that the real score may have changed since
the PR was raised.
> - This PR was automatically created by Snyk using the credentials of a
real user.

---

**Note:** _You are seeing this because you or someone else with access
to this repository has authorized Snyk to open fix PRs._

For more information: <img
src="https://api.segment.io/v1/pixel/track?data=eyJ3cml0ZUtleSI6InJyWmxZcEdHY2RyTHZsb0lYd0dUcVg4WkFRTnNCOUEwIiwiYW5vbnltb3VzSWQiOiI1YWE0Mzc4Yi1kNzA2LTRmYWEtYTAzNC04NThhYTYwNDhhOWIiLCJldmVudCI6IlBSIHZpZXdlZCIsInByb3BlcnRpZXMiOnsicHJJZCI6IjVhYTQzNzhiLWQ3MDYtNGZhYS1hMDM0LTg1OGFhNjA0OGE5YiJ9fQ=="
width="0" height="0"/>
🧐 [View latest project
report](https://app.snyk.io/org/compbio/project/c80293d7-c0f4-4d94-b297-efe1fc5caf56?utm_source&#x3D;github&amp;utm_medium&#x3D;referral&amp;page&#x3D;fix-pr)
📜 [Customise PR
templates](https://docs.snyk.io/scan-using-snyk/pull-requests/snyk-fix-pull-or-merge-requests/customize-pr-templates?utm_source=github&utm_content=fix-pr-template)
🛠 [Adjust project
settings](https://app.snyk.io/org/compbio/project/c80293d7-c0f4-4d94-b297-efe1fc5caf56?utm_source&#x3D;github&amp;utm_medium&#x3D;referral&amp;page&#x3D;fix-pr/settings)
📚 [Read about Snyk's upgrade
logic](https://docs.snyk.io/scan-with-snyk/snyk-open-source/manage-vulnerabilities/upgrade-package-versions-to-fix-vulnerabilities?utm_source=github&utm_content=fix-pr-template)

---

**Learn how to fix vulnerabilities with free interactive lessons:**

🦉 [Out-of-bounds
Write](https://learn.snyk.io/lesson/out-of-bounds-write/?loc&#x3D;fix-pr)
🦉 [Directory
Traversal](https://learn.snyk.io/lesson/directory-traversal/?loc&#x3D;fix-pr)

[//]: #
'snyk:metadata:{"breakingChangeRiskLevel":null,"FF_showPullRequestBreakingChanges":false,"FF_showPullRequestBreakingChangesWebSearch":false,"customTemplate":{"variablesUsed":[],"fieldsUsed":[]},"dependencies":[{"name":"ubuntu","from":"noble-20250925","to":"24.04"}],"env":"prod","issuesToFix":["SNYK-UBUNTU2404-GNUPG2-14849555","SNYK-UBUNTU2404-PAM-11936905","SNYK-UBUNTU2404-PAM-11936905","SNYK-UBUNTU2404-PAM-11936905","SNYK-UBUNTU2404-PAM-11936905"],"prId":"5aa4378b-d706-4faa-a034-858aa6048a9b","prPublicId":"5aa4378b-d706-4faa-a034-858aa6048a9b","packageManager":"dockerfile","priorityScoreList":[281,231],"projectPublicId":"c80293d7-c0f4-4d94-b297-efe1fc5caf56","projectUrl":"https://app.snyk.io/org/compbio/project/c80293d7-c0f4-4d94-b297-efe1fc5caf56?utm_source=github&utm_medium=referral&page=fix-pr","prType":"fix","templateFieldSources":{"branchName":"default","commitMessage":"default","description":"default","title":"default"},"templateVariants":["updated-fix-title","priorityScore"],"type":"auto","upgrade":["SNYK-UBUNTU2404-GNUPG2-14849555","SNYK-UBUNTU2404-PAM-11936905","SNYK-UBUNTU2404-PAM-11936905","SNYK-UBUNTU2404-PAM-11936905","SNYK-UBUNTU2404-PAM-11936905"],"vulns":["SNYK-UBUNTU2404-GNUPG2-14849555","SNYK-UBUNTU2404-PAM-11936905"],"patch":[],"isBreakingChange":false,"remediationStrategy":"vuln"}'

---------

Co-authored-by: snyk-bot <snyk-bot@snyk.io>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: adthrasher <1165729+adthrasher@users.noreply.github.com>
Co-authored-by: Andrew Thrasher <adthrasher@gmail.com>

Author: 4 people

data_structures/flag_filter.wdl

@@ -106,7 +106,7 @@ task validate_string_is_12bit_int {
     >>>
 
     runtime {
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }

data_structures/read_group.wdl

@@ -138,7 +138,7 @@ task get_read_groups {
 
     runtime {
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }
@@ -363,7 +363,7 @@ task validate_read_group {
     >>>
 
     runtime {
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }
@@ -421,7 +421,7 @@ task inner_read_group_to_string {
     }
 
     runtime {
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }

docker/python-plotting/package.json

@@ -1,4 +1,4 @@
 {
     "name": "python-plotting",
-    "version": "2.0.7"
+    "version": "2.0.8"
 }

docker/umap/Dockerfile

@@ -1,10 +1,10 @@
-FROM python:3.13.1-alpine
+FROM python:3.14.2-alpine
 
-# Downstream requires llvm15, but that is out-of-date
-# llvm15 installs with the -15 suffix, so we need to symlink
-RUN apk add --no-cache build-base llvm15-dev bash \
-    && ln -s /usr/bin/llvm-config-15 /usr/bin/llvm-config
+# Downstream requires llvm20, but that is out-of-date
+# llvm20 installs with the -20 suffix, so we need to symlink
+RUN apk add --no-cache build-base llvm20-dev bash cmake llvm20 llvm20-libs llvm20-static llvm20-gtest \
+    && ln -s /usr/bin/llvm20-config /usr/bin/llvm-config
 
-RUN pip install umap-learn==0.5.7 pandas
+RUN pip install umap-learn==0.5.11 pandas
 
 COPY --from=scripts --chmod=777 methylation/generate_umap.py /scripts/methylation/generate_umap.py

docker/umap/package.json

@@ -1,5 +1,5 @@
 {
     "name": "umap",
     "version": "0.5.7",
-    "revision": "10"
+    "revision": "11"
 }

docker/util/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:noble-20250925
+FROM ubuntu:noble-20260113
 
 RUN apt-get update \
     && apt-get upgrade -y \

docker/util/package.json

@@ -1,4 +1,4 @@
 {
     "name": "util",
-    "version": "3.0.1"
+    "version": "3.0.2"
 }

tools/htseq.wdl

@@ -195,7 +195,7 @@ task calc_tpm {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }

tools/md5sum.wdl

@@ -34,7 +34,7 @@ task compute_checksum {
 
     runtime {
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }

tools/util.wdl

@@ -40,7 +40,7 @@ task download {
 
     runtime {
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }
@@ -79,7 +79,7 @@ task split_string {
     }
 
     runtime {
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }
@@ -127,7 +127,7 @@ task calc_feature_lengths {
     runtime {
         memory: "16 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }
@@ -246,7 +246,7 @@ task unpack_tarball {
 
     runtime {
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }
@@ -353,7 +353,7 @@ task global_phred_scores {
     runtime {
         memory: "4 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }
@@ -402,7 +402,7 @@ task check_fastq_and_rg_concordance {
     >>>
 
     runtime {
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }
@@ -462,7 +462,7 @@ task split_fastq {
         cpu: ncpu
         memory: "4 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:3.0.1"
+        container: "ghcr.io/stjudecloud/util:3.0.2"
         maxRetries: 1
     }
 }