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[Snyk] Security upgrade ubuntu from noble-20250925 to noble-20260113 #288

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Merged
adthrasher merged 6 commits into from
Feb 9, 2026
Merged

[Snyk] Security upgrade ubuntu from noble-20250925 to noble-20260113 #288

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653cc1d
fix: docker/util/Dockerfile to reduce vulnerabilities
snyk-bot Jan 17, 2026
2c2bafc
Bump util Docker image version for Ubuntu 24.04 base upgrade (#289)
Copilot Jan 21, 2026
d154d43
Use date stamped image
adthrasher Feb 6, 2026
cfa95bd
chore: bump python-plotting
adthrasher Feb 6, 2026
693a469
[Snyk] Security upgrade python from 3.13.1-alpine to 3.14.2-alpine (#…
kevin-benton Feb 6, 2026
5084fd1
chore: bump umap version
adthrasher Feb 6, 2026
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2 changes: 1 addition & 1 deletion data_structures/flag_filter.wdl
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Expand Up @@ -107,7 +107,7 @@ 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
}
}
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6 changes: 3 additions & 3 deletions data_structures/read_group.wdl
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Expand Up @@ -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
}
}
Expand Down Expand Up @@ -356,7 +356,7 @@ task validate_read_group {
>>>

runtime {
container: "ghcr.io/stjudecloud/util:3.0.1"
container: "ghcr.io/stjudecloud/util:3.0.2"
maxRetries: 1
}
}
Expand Down Expand Up @@ -412,7 +412,7 @@ 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
}
}
2 changes: 1 addition & 1 deletion docker/python-plotting/package.json
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@@ -1,4 +1,4 @@
{
"name": "python-plotting",
"version": "2.0.7"
"version": "2.0.8"
}
12 changes: 6 additions & 6 deletions docker/umap/Dockerfile
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@@ -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# Downstream requires llvm15, but that is out-of-date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
2 changes: 1 addition & 1 deletion docker/umap/package.json
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@@ -1,5 +1,5 @@
{
"name": "umap",
"version": "0.5.7",
"revision": "10"
"revision": "11"
}
2 changes: 1 addition & 1 deletion docker/util/Dockerfile
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@@ -1,4 +1,4 @@
FROM ubuntu:noble-20250925
FROM ubuntu:noble-20260113

Check failure

Code scanning / Snyk Container

Low severity - Out-of-Bounds vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a low severity vulnerability.

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Low severity - Out-of-Bounds vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a low severity vulnerability.

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Low severity - Use After Free vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a low severity vulnerability.

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Low severity - Buffer Overflow vulnerability in icu High

This file introduces a vulnerable icu package with a low severity vulnerability.

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Medium severity - Out-of-bounds Read vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Low severity - Out-of-Bounds vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a low severity vulnerability.

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Medium severity - Out-of-Bounds vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Medium severity - Out-of-bounds Read vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Medium severity - Use After Free vulnerability in libxslt High

This file introduces a vulnerable libxslt package with a medium severity vulnerability.

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Low severity - Allocation of Resources Without Limits or Throttling vulnerability in glibc High

This file introduces a vulnerable glibc package with a low severity vulnerability.

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Medium severity - XML Injection vulnerability in fonttools Critical

This file introduces a vulnerable fonttools package with a medium severity vulnerability.

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Medium severity - Out-of-bounds Write vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Medium severity - Out-of-bounds Write vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Medium severity - Out-of-bounds Write vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Medium severity - Directory Traversal vulnerability in pam High

This file introduces a vulnerable pam package with a medium severity vulnerability.

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Low severity - Out-of-bounds Read vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a low severity vulnerability.

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Low severity - Double Free vulnerability in patch High

This file introduces a vulnerable patch package with a low severity vulnerability.

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Medium severity - Improper Handling of Highly Compressed Data (Data Amplification) vulnerability in python-pip High

This file introduces a vulnerable python-pip package with a medium severity vulnerability.

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Medium severity - Allocation of Resources Without Limits or Throttling vulnerability in python-pip High

This file introduces a vulnerable python-pip package with a medium severity vulnerability.

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Medium severity - Improper Handling of Highly Compressed Data (Data Amplification) vulnerability in python-pip High

This file introduces a vulnerable python-pip package with a medium severity vulnerability.

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Low severity - Out-of-bounds Read vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a low severity vulnerability.

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Low severity - Out-of-bounds Read vulnerability in hdf5 Critical

This file introduces a vulnerable hdf5 package with a low severity vulnerability.

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Medium severity - Out-of-bounds Read vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Medium severity - Out-of-Bounds vulnerability in hdf5 High

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Code scanning / Snyk Container

Medium severity - NULL Pointer Dereference vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Medium severity - Out-of-bounds Write vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Code scanning / Snyk Container

Medium severity - Out-of-bounds Write vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Medium severity - Use After Free vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Code scanning / Snyk Container

Medium severity - Out-of-bounds Write vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Low severity - Race Condition vulnerability in htslib Medium

This file introduces a vulnerable htslib package with a low severity vulnerability.

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Medium severity - CVE-2024-38949 vulnerability in libde265 Warning

This file introduces a vulnerable libde265 package with a medium severity vulnerability.

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Medium severity - CVE-2024-38950 vulnerability in libde265 Warning

This file introduces a vulnerable libde265 package with a medium severity vulnerability.

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Medium severity - Out-of-bounds Read vulnerability in libheif Warning

This file introduces a vulnerable libheif package with a medium severity vulnerability.

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Medium severity - Expired Pointer Dereference vulnerability in libxslt Medium

This file introduces a vulnerable libxslt package with a medium severity vulnerability.

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Low severity - Allocation of Resources Without Limits or Throttling vulnerability in openjpeg2 Medium

This file introduces a vulnerable openjpeg2 package with a low severity vulnerability.

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Medium severity - Resource Exhaustion vulnerability in openjpeg2 Warning

This file introduces a vulnerable openjpeg2 package with a medium severity vulnerability.

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Medium severity - Resource Exhaustion vulnerability in openjpeg2 Warning

This file introduces a vulnerable openjpeg2 package with a medium severity vulnerability.

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Low severity - Release of Invalid Pointer or Reference vulnerability in patch Medium

This file introduces a vulnerable patch package with a low severity vulnerability.

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Medium severity - CVE-2023-45803 vulnerability in python-pip Medium

This file introduces a vulnerable python-pip package with a medium severity vulnerability.

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Medium severity - CVE-2024-35195 vulnerability in python-pip Warning

This file introduces a vulnerable python-pip package with a medium severity vulnerability.

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Medium severity - Directory Traversal vulnerability in tar Warning

This file introduces a vulnerable tar package with a medium severity vulnerability.

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Medium severity - Open Redirect vulnerability in wget Medium

This file introduces a vulnerable wget package with a medium severity vulnerability.

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Medium severity - Out-of-Bounds vulnerability in binutils Medium

This file introduces a vulnerable binutils package with a medium severity vulnerability.

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Low severity - Allocation of Resources Without Limits or Throttling vulnerability in binutils Medium

This file introduces a vulnerable binutils package with a low severity vulnerability.

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Low severity - Improper Input Validation vulnerability in coreutils Medium

This file introduces a vulnerable coreutils package with a low severity vulnerability.

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Medium severity - Algorithmic Complexity vulnerability in expat Medium

This file introduces a vulnerable expat package with a medium severity vulnerability.

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Medium severity - Improper Verification of Cryptographic Signature vulnerability in gnupg2 Medium

This file introduces a vulnerable gnupg2 package with a medium severity vulnerability.

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Medium severity - Out-of-Bounds vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Low severity - Improper Resource Shutdown or Release vulnerability in hdf5 Medium

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Medium severity - Out-of-Bounds vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Medium severity - Out-of-bounds Read vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Medium severity - NULL Pointer Dereference vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Low severity - Out-of-bounds Write vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a low severity vulnerability.

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Medium severity - Divide By Zero vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Medium severity - Out-of-bounds Read vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Code scanning / Snyk Container

Medium severity - Out-of-Bounds vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Code scanning / Snyk Container

Medium severity - Out-of-Bounds vulnerability in hdf5 Medium

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Code scanning / Snyk Container

Medium severity - Out-of-bounds Write vulnerability in hdf5 Low

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Code scanning / Snyk Container

Low severity - CVE-2024-56433 vulnerability in shadow Note

This file introduces a vulnerable shadow package with a low severity vulnerability.

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Low severity - Memory Leak vulnerability in binutils Low

This file introduces a vulnerable binutils package with a low severity vulnerability.

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Medium severity - Out-of-Bounds vulnerability in binutils Low

This file introduces a vulnerable binutils package with a medium severity vulnerability.

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Medium severity - Out-of-Bounds vulnerability in hdf5 Low

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.

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Code scanning / Snyk Container

Low severity - Out-of-bounds Read vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.

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Low severity - CVE-2025-10148 vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.

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Low severity - CVE-2025-15224 vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.

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Low severity - CVE-2025-15079 vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.

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Low severity - CVE-2025-14819 vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.

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Low severity - CVE-2024-41996 vulnerability in openssl Note

This file introduces a vulnerable openssl package with a low severity vulnerability.

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Low severity - Open Redirect vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.

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Low severity - CVE-2025-0167 vulnerability in curl Note

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Low severity - Out-of-Bounds vulnerability in hdf5 Low

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Low severity - Resource Exhaustion vulnerability in hdf5 Low

This file introduces a vulnerable hdf5 package with a low severity vulnerability.

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Code scanning / Snyk Container

Low severity - Out-of-bounds Write vulnerability in gnupg2 Low

This file introduces a vulnerable gnupg2 package with a low severity vulnerability.

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Low severity - CVE-2024-25269 vulnerability in libheif Note

This file introduces a vulnerable libheif package with a low severity vulnerability.

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Low severity - NULL Pointer Dereference vulnerability in harfbuzz Note

This file introduces a vulnerable harfbuzz package with a low severity vulnerability.

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Low severity - Information Exposure vulnerability in libgcrypt20 Note

This file introduces a vulnerable libgcrypt20 package with a low severity vulnerability.

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Medium severity - Out-of-bounds Write vulnerability in hdf5 Low

This file introduces a vulnerable hdf5 package with a medium severity vulnerability.
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@a-frantz a-frantz Feb 9, 2026

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Why is this date pinned?

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@adthrasher adthrasher Feb 9, 2026

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I made that switch in #274. Ubuntu only uses major+minor pairs. When they release (what I assume is a patched version), they overwrite the existing image. So I switched to the date-stamped images to avoid the image changing out from under us.

% docker run --rm -it ubuntu:noble-20250925 cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=24.04
DISTRIB_CODENAME=noble
DISTRIB_DESCRIPTION="Ubuntu 24.04.3 LTS"

% docker run --rm -it ubuntu:noble-20260113  cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=24.04
DISTRIB_CODENAME=noble
DISTRIB_DESCRIPTION="Ubuntu 24.04.3 LTS"


RUN apt-get update \
&& apt-get upgrade -y \
Expand Down
2 changes: 1 addition & 1 deletion docker/util/package.json
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@@ -1,4 +1,4 @@
{
"name": "util",
"version": "3.0.1"
"version": "3.0.2"
}
2 changes: 1 addition & 1 deletion tools/htseq.wdl
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Expand Up @@ -190,7 +190,7 @@ 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
}
}
2 changes: 1 addition & 1 deletion tools/md5sum.wdl
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Expand Up @@ -35,7 +35,7 @@ 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
}
}
14 changes: 7 additions & 7 deletions tools/util.wdl
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Expand Up @@ -41,7 +41,7 @@ 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
}
}
Expand Down Expand Up @@ -80,7 +80,7 @@ task split_string {
}

runtime {
container: "ghcr.io/stjudecloud/util:3.0.1"
container: "ghcr.io/stjudecloud/util:3.0.2"
maxRetries: 1
}
}
Expand Down Expand Up @@ -128,7 +128,7 @@ 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
}
}
Expand Down Expand Up @@ -247,7 +247,7 @@ 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
}
}
Expand Down Expand Up @@ -351,7 +351,7 @@ 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
}
}
Expand Down Expand Up @@ -398,7 +398,7 @@ 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
}
}
Expand Down Expand Up @@ -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
}
}
2 changes: 1 addition & 1 deletion workflows/dnaseq/dnaseq-standard.wdl
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Expand Up @@ -158,7 +158,7 @@ task parse_input {
>>>

runtime {
container: "ghcr.io/stjudecloud/util:3.0.1"
container: "ghcr.io/stjudecloud/util:3.0.2"
maxRetries: 1
}
}
4 changes: 2 additions & 2 deletions workflows/methylation/methylation-cohort.wdl
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Expand Up @@ -285,7 +285,7 @@ task generate_umap {
}

runtime {
container: "ghcr.io/stjudecloud/umap:0.5.7-10"
container: "ghcr.io/stjudecloud/umap:0.5.7-11"
memory: "8 GB"
cpu: 1
disks: "~{disk_size_gb} GB"
Expand Down Expand Up @@ -325,7 +325,7 @@ task plot_umap {
cpu: 1
memory: "4 GB"
disks: "4 GB"
container: "ghcr.io/stjudecloud/python-plotting:2.0.7"
container: "ghcr.io/stjudecloud/python-plotting:2.0.8"
maxRetries: 1
}
}
2 changes: 1 addition & 1 deletion workflows/qc/quality-check-standard.wdl
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Expand Up @@ -547,7 +547,7 @@ task parse_input {
}

runtime {
container: "ghcr.io/stjudecloud/util:3.0.1"
container: "ghcr.io/stjudecloud/util:3.0.2"
maxRetries: 1
}
}
2 changes: 1 addition & 1 deletion workflows/rnaseq/rnaseq-standard.wdl
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Expand Up @@ -181,7 +181,7 @@ task parse_input {
>>>

runtime {
container: "ghcr.io/stjudecloud/util:3.0.1"
container: "ghcr.io/stjudecloud/util:3.0.2"
maxRetries: 1
}
}
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