diff --git a/.github/workflows/docker-clean.yaml b/.github/workflows/docker-clean.yaml
index ba5c4023..7b885a49 100644
--- a/.github/workflows/docker-clean.yaml
+++ b/.github/workflows/docker-clean.yaml
@@ -40,7 +40,7 @@ jobs:
             run: | # NOTE: This will delete any images for branch names that contain the current branch name as a prefix.
                REF="${{ github.event.ref }}"
                REF="${REF##*/}"
-               gh api /orgs/${{ github.repository_owner }}/packages/container/${{ env.TOOL }}/versions | jq -r '.[] | select(isempty(.metadata.container.tags[]) or (.metadata.container.tags[] | contains("branch-${REF}"))) | .id' > versions.txt
+               gh api --paginate /orgs/${{ github.repository_owner }}/packages/container/${{ env.TOOL }}/versions | jq -r '.[] | select(isempty(.metadata.container.tags[]) or (.metadata.container.tags[] | contains("branch-${REF}"))) | .id' > versions.txt
                echo "IDS=$(tr -s '\n' ',' < versions.txt | sed 's/,$//')" >> $GITHUB_ENV
           - uses: actions/delete-package-versions@v5
             with: 
diff --git a/data_structures/flag_filter.wdl b/data_structures/flag_filter.wdl
index 0b9d39ed..88f811f6 100644
--- a/data_structures/flag_filter.wdl
+++ b/data_structures/flag_filter.wdl
@@ -118,7 +118,7 @@ task validate_string_is_12bit_oct_dec_or_hex {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 1
     }
 }
diff --git a/data_structures/read_group.wdl b/data_structures/read_group.wdl
index 94a655c4..c4461597 100644
--- a/data_structures/read_group.wdl
+++ b/data_structures/read_group.wdl
@@ -104,7 +104,7 @@ task read_group_to_string {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 1
     }
 }
@@ -441,7 +441,7 @@ task validate_read_group {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 0
     }
 }
diff --git a/docker/estimate/Dockerfile b/docker/estimate/Dockerfile
index 9a189946..eb4a7a05 100644
--- a/docker/estimate/Dockerfile
+++ b/docker/estimate/Dockerfile
@@ -1,3 +1,5 @@
-FROM r-base:4.0.3
+FROM ghcr.io/r-hub/r-minimal/r-minimal:4.4.2
+
+RUN apk upgrade --no-cache
 
 RUN R -e 'install.packages("estimate", repos="http://r-forge.r-project.org", dependencies=TRUE)'
diff --git a/docker/estimate/package.json b/docker/estimate/package.json
index 2e5d6117..cd5a502f 100644
--- a/docker/estimate/package.json
+++ b/docker/estimate/package.json
@@ -1,4 +1,4 @@
 {
     "name": "estimate",
-    "version": "1.1.1"
+    "version": "2.0.0"
 }
\ No newline at end of file
diff --git a/docker/python-plotting/Dockerfile b/docker/python-plotting/Dockerfile
index d7f94886..3548be9b 100644
--- a/docker/python-plotting/Dockerfile
+++ b/docker/python-plotting/Dockerfile
@@ -1,4 +1,6 @@
-FROM python:3.13.0
+FROM python:3.13.1-alpine
+
+RUN apk add --no-cache bash
 
 RUN pip install pandas numpy matplotlib seaborn plotly
 
diff --git a/docker/python-plotting/package.json b/docker/python-plotting/package.json
index 7dbffa54..26ec26a4 100644
--- a/docker/python-plotting/package.json
+++ b/docker/python-plotting/package.json
@@ -1,4 +1,4 @@
 {
     "name": "python-plotting",
-    "version": "1.2.1"
+    "version": "2.0.0"
 }
\ No newline at end of file
diff --git a/docker/umap/Dockerfile b/docker/umap/Dockerfile
index d9f689fc..e0e13b4b 100644
--- a/docker/umap/Dockerfile
+++ b/docker/umap/Dockerfile
@@ -1,4 +1,9 @@
-FROM python:3.12.7
+FROM python:3.13.1-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
 
 RUN pip install umap-learn==0.5.7 pandas
 
diff --git a/docker/umap/package.json b/docker/umap/package.json
index bdfac4ee..d0687563 100644
--- a/docker/umap/package.json
+++ b/docker/umap/package.json
@@ -1,5 +1,5 @@
 {
     "name": "umap",
     "version": "0.5.7",
-    "revision": "3"
+    "revision": "4"
 }
\ No newline at end of file
diff --git a/docker/util/Dockerfile b/docker/util/Dockerfile
index 40c8e484..fc6bf712 100644
--- a/docker/util/Dockerfile
+++ b/docker/util/Dockerfile
@@ -1,7 +1,8 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 
 RUN apt-get update \
     && apt-get upgrade -y \
-    && apt-get install wget zip gcc zlib1g-dev libbz2-dev liblzma-dev jq python3 python3-pip parallel -y \
-    && rm -r /var/lib/apt/lists/* \
-    && python3 -m pip --no-cache-dir install csvkit pysam
+    &&  apt-get install wget zip gcc zlib1g-dev libbz2-dev \
+      liblzma-dev jq python3 python3-pip parallel \
+      python3-csvkit python3-pysam -y \
+    && rm -r /var/lib/apt/lists/*
diff --git a/docker/util/package.json b/docker/util/package.json
index b6f363b2..19bbebcd 100644
--- a/docker/util/package.json
+++ b/docker/util/package.json
@@ -1,4 +1,4 @@
 {
     "name": "util",
-    "version": "1.5.1"
+    "version": "2.0.0"
 }
\ No newline at end of file
diff --git a/tests/tools/test_arriba.yaml b/tests/tools/test_arriba.yaml
index 52cdf7fc..770a1300 100644
--- a/tests/tools/test_arriba.yaml
+++ b/tests/tools/test_arriba.yaml
@@ -3,7 +3,7 @@
     - miniwdl
     - arriba
   command: >-
-    miniwdl run -d test-output/. --task arriba -i tests/tools/input_json/arriba.json tools/arriba.wdl
+    miniwdl run --verbose -d test-output/. --task arriba -i tests/tools/input_json/arriba.json tools/arriba.wdl
   files:
     - path: test-output/out/fusions/fusions.tsv
     - path: test-output/out/discarded_fusions/fusions.discarded.tsv
@@ -13,7 +13,7 @@
     - miniwdl
     - arriba
   command: >-
-    miniwdl run -d test-output/. --task arriba_tsv_to_vcf tools/arriba.wdl fusions="tests/input/fusions.tsv" reference_fasta="tests/input/GRCh38.chr9_chr22.fa.gz"
+    miniwdl run --verbose -d test-output/. --task arriba_tsv_to_vcf tools/arriba.wdl fusions="tests/input/fusions.tsv" reference_fasta="tests/input/GRCh38.chr9_chr22.fa.gz"
   files:
     - path: test-output/out/fusions_vcf/fusions.vcf
 
@@ -22,7 +22,7 @@
     - miniwdl
     - arriba
   command: >-
-    miniwdl run -d test-output/. --task arriba_extract_fusion_supporting_alignments tools/arriba.wdl fusions="tests/input/fusions.tsv" bam="tests/input/Aligned.sortedByCoord.chr9_chr22.bam" bam_index="tests/input/Aligned.sortedByCoord.chr9_chr22.bam.bai"
+    miniwdl run --verbose -d test-output/. --task arriba_extract_fusion_supporting_alignments tools/arriba.wdl fusions="tests/input/fusions.tsv" bam="tests/input/Aligned.sortedByCoord.chr9_chr22.bam" bam_index="tests/input/Aligned.sortedByCoord.chr9_chr22.bam.bai"
   files:
     - path: test-output/out/fusion_bams/0/fusions_1.bam
 
@@ -31,6 +31,6 @@
     - miniwdl
     - arriba
   command: >-
-    miniwdl run -d test-output/. --task arriba_annotate_exon_numbers tools/arriba.wdl fusions="tests/input/fusions.tsv" gtf="tests/input/gencode.v31.chr9_chr22.gtf.gz"
+    miniwdl run --verbose -d test-output/. --task arriba_annotate_exon_numbers tools/arriba.wdl fusions="tests/input/fusions.tsv" gtf="tests/input/gencode.v31.chr9_chr22.gtf.gz"
   files:
     - path: test-output/out/fusion_tsv/fusions.annotated.tsv
diff --git a/tests/tools/test_picard.yaml b/tests/tools/test_picard.yaml
index 6fc8f557..966a3d69 100644
--- a/tests/tools/test_picard.yaml
+++ b/tests/tools/test_picard.yaml
@@ -121,7 +121,7 @@
     - miniwdl
     - picard
   command: >-
-    miniwdl run -d test-output/. --task merge_vcfs -i tests/tools/input_json/picard_merge_vcfs.json tools/picard.wdl
+    miniwdl run --verbose -d test-output/. --task merge_vcfs -i tests/tools/input_json/picard_merge_vcfs.json tools/picard.wdl
   files:
     - path: test-output/out/merged_vcf/test.vcf.gz
 
@@ -130,7 +130,7 @@
     - miniwdl
     - picard
   command: >-
-    miniwdl run -d test-output/. --task scatter_interval_list tools/picard.wdl interval_list="tests/input/wgs_calling_regions.hg38.interval_list" scatter_count=3
+    miniwdl run --verbose -d test-output/. --task scatter_interval_list tools/picard.wdl interval_list="tests/input/wgs_calling_regions.hg38.interval_list" scatter_count=3
   files:
     - path: test-output/out/interval_lists_scatter/0/1scattered.interval_list
     - path: test-output/out/interval_lists_scatter/1/2scattered.interval_list
@@ -141,6 +141,6 @@
     - miniwdl
     - picard
   command: >-
-    miniwdl run -d test-output/. --task create_sequence_dictionary tools/picard.wdl fasta="tests/input/GRCh38.chrY_chrM.fa" outfile_name="GRCh38.chrY_chrM.dict"
+    miniwdl run --verbose -d test-output/. --task create_sequence_dictionary tools/picard.wdl fasta="tests/input/GRCh38.chrY_chrM.fa" outfile_name="GRCh38.chrY_chrM.dict"
   files:
     - path: test-output/out/dictionary/GRCh38.chrY_chrM.dict
\ No newline at end of file
diff --git a/tests/tools/test_sambamba.yaml b/tests/tools/test_sambamba.yaml
index c893a503..cf1c486f 100644
--- a/tests/tools/test_sambamba.yaml
+++ b/tests/tools/test_sambamba.yaml
@@ -3,7 +3,7 @@
     - miniwdl
     - sambamba
   command: >-
-    miniwdl run -d test-output/. --task index tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
+    miniwdl run --verbose -d test-output/. --task index tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
     - path: test-output/out/bam_index/test.bwa_aln_pe.chrY_chrM.bam.bai
 
@@ -12,7 +12,7 @@
     - miniwdl
     - sambamba
   command: >-
-    miniwdl run -d test-output/. --task merge -i tests/tools/input_json/sambamba_merge.json tools/sambamba.wdl
+    miniwdl run --verbose -d test-output/. --task merge -i tests/tools/input_json/sambamba_merge.json tools/sambamba.wdl
   files:
     - path: test-output/out/merged_bam/test.bam
 
@@ -21,7 +21,7 @@
     - miniwdl
     - sambamba
   command: >-
-    miniwdl run -d test-output/. --task sort tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
+    miniwdl run --verbose -d test-output/. --task sort tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
     - path: test-output/out/sorted_bam/test.bwa_aln_pe.chrY_chrM.sorted.bam
 
@@ -30,7 +30,7 @@
     - miniwdl
     - sambamba
   command: >-
-    miniwdl run -d test-output/. --task flagstat tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
+    miniwdl run --verbose -d test-output/. --task flagstat tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
     - path: test-output/out/flagstat_report/test.bwa_aln_pe.chrY_chrM.flagstat.txt
 
@@ -39,7 +39,7 @@
     - miniwdl
     - sambamba
   command: >-
-    miniwdl run -d test-output/. --task markdup tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
+    miniwdl run --verbose -d test-output/. --task markdup tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
     - path: test-output/out/duplicate_marked_bam/test.bwa_aln_pe.chrY_chrM.markdup.bam
     - path: test-output/out/duplicate_marked_bam_index/test.bwa_aln_pe.chrY_chrM.markdup.bam.bai
diff --git a/tests/tools/test_samtools.yaml b/tests/tools/test_samtools.yaml
index e5652b2a..39a69961 100644
--- a/tests/tools/test_samtools.yaml
+++ b/tests/tools/test_samtools.yaml
@@ -110,6 +110,6 @@
     - miniwdl
     - samtools
   command: >-
-    miniwdl run -d test-output/. --task faidx tools/samtools.wdl fasta="tests/input/test.fa"
+    miniwdl run --verbose -d test-output/. --task faidx tools/samtools.wdl fasta="tests/input/test.fa"
   files:
     - path: test-output/out/fasta_index/test.fa.fai
diff --git a/tests/tools/test_util.yaml b/tests/tools/test_util.yaml
index 142b8fd3..49058ee6 100644
--- a/tests/tools/test_util.yaml
+++ b/tests/tools/test_util.yaml
@@ -128,6 +128,6 @@
     - miniwdl
     - util
   command: >-
-    miniwdl run -d test-output/. --task split_fastq tools/util.wdl fastq="tests/input/test_R1.fq.gz" prefix="test.R1."
+    miniwdl run --verbose -d test-output/. --task split_fastq tools/util.wdl fastq="tests/input/test_R1.fq.gz" prefix="test.R1."
   files:
     - path: "test-output/out/fastqs/0/test.R1.000000.fastq.gz"
\ No newline at end of file
diff --git a/tests/workflows/test-methylation-cohort.yaml b/tests/workflows/test-methylation-cohort.yaml
index b9a5bd0c..32eb7d2c 100644
--- a/tests/workflows/test-methylation-cohort.yaml
+++ b/tests/workflows/test-methylation-cohort.yaml
@@ -3,7 +3,7 @@
     - miniwdl
     - methylation
   command: >-
-    miniwdl run -d test-output/. --task combine_data -i tests/workflows/input_json/combine_data.json workflows/methylation/methylation-cohort.wdl
+    miniwdl run --verbose -d test-output/. --task combine_data -i tests/workflows/input_json/combine_data.json workflows/methylation/methylation-cohort.wdl
   files:
     - path: test-output/out/combined_beta/combined_beta.csv
 
@@ -12,7 +12,7 @@
     - miniwdl
     - methylation
   command: >-
-    miniwdl run -d test-output/. --task filter_probes -i tests/workflows/input_json/filter_probes.json workflows/methylation/methylation-cohort.wdl
+    miniwdl run --verbose -d test-output/. --task filter_probes -i tests/workflows/input_json/filter_probes.json workflows/methylation/methylation-cohort.wdl
   files:
     - path: test-output/out/filtered_beta_values/filtered.beta.csv
     - path: test-output/out/filtered_probes/filtered.probes.csv
@@ -22,7 +22,7 @@
     - miniwdl
     - methylation
   command: >-
-    miniwdl run -d test-output/. --task generate_umap -i tests/workflows/input_json/generate_umap.json workflows/methylation/methylation-cohort.wdl
+    miniwdl run --verbose -d test-output/. --task generate_umap -i tests/workflows/input_json/generate_umap.json workflows/methylation/methylation-cohort.wdl
   files:
     - path: test-output/out/umap/umap.csv
 
@@ -31,6 +31,6 @@
     - miniwdl
     - methylation
   command: >-
-    miniwdl run -d test-output/. --task plot_umap -i tests/workflows/input_json/plot_umap.json workflows/methylation/methylation-cohort.wdl
+    miniwdl run --verbose -d test-output/. --task plot_umap -i tests/workflows/input_json/plot_umap.json workflows/methylation/methylation-cohort.wdl
   files:
     - path: test-output/out/umap_plot/umap.png
diff --git a/tests/workflows/test-methylation-preprocess.yaml b/tests/workflows/test-methylation-preprocess.yaml
index d098f4b2..6b17fba1 100644
--- a/tests/workflows/test-methylation-preprocess.yaml
+++ b/tests/workflows/test-methylation-preprocess.yaml
@@ -3,7 +3,7 @@
     - miniwdl
     - methylation
   command: >-
-    miniwdl run -d test-output/. --task process_raw_idats -i tests/workflows/input_json/process_raw_idats.json workflows/methylation/methylation-preprocess.wdl
+    miniwdl run --verbose -d test-output/. --task process_raw_idats -i tests/workflows/input_json/process_raw_idats.json workflows/methylation/methylation-preprocess.wdl
   files:
     - path: test-output/out/beta_swan_norm_unfiltered/201533520001_R03C01.beta_swan_norm_unfiltered.csv
     - path: test-output/out/beta_swan_norm_unfiltered_genomic/201533520001_R03C01.beta_swan_norm_unfiltered.genomic.csv
diff --git a/tools/bwa.wdl b/tools/bwa.wdl
index a9cdefc0..000f1680 100644
--- a/tools/bwa.wdl
+++ b/tools/bwa.wdl
@@ -86,7 +86,7 @@ task bwa_aln {
         cpu: ncpu
         memory: "5 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/bwa:0.7.17-2"
+        container: "ghcr.io/stjudecloud/bwa:branch-update_images-0.7.17-2"
         maxRetries: 1
     }
 }
@@ -187,7 +187,7 @@ task bwa_aln_pe {
         cpu: ncpu
         memory: "17 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/bwa:0.7.17-2"
+        container: "ghcr.io/stjudecloud/bwa:branch-update_images-0.7.17-2"
         maxRetries: 1
     }
 }
@@ -283,7 +283,7 @@ task bwa_mem {
         cpu: ncpu
         memory: "25 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/bwa:0.7.17-2"
+        container: "ghcr.io/stjudecloud/bwa:branch-update_images-0.7.17-2"
         maxRetries: 1
     }
 }
@@ -334,7 +334,7 @@ task build_bwa_db {
     runtime {
         memory: "5 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/bwa:0.7.17-2"
+        container: "ghcr.io/stjudecloud/bwa:branch-update_images-0.7.17-2"
         maxRetries: 1
     }
 }
diff --git a/tools/estimate.wdl b/tools/estimate.wdl
index 89054553..62c7b5ca 100644
--- a/tools/estimate.wdl
+++ b/tools/estimate.wdl
@@ -51,7 +51,7 @@ task run_estimate {
     runtime {
         memory: "~{memory_gb} GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/estimate:1.1.1"
+        container: "ghcr.io/stjudecloud/estimate:branch-update_images-2.0.0"
         maxRetries: max_retries
     }
 }
diff --git a/tools/htseq.wdl b/tools/htseq.wdl
index 6069a815..1cafc101 100755
--- a/tools/htseq.wdl
+++ b/tools/htseq.wdl
@@ -209,7 +209,7 @@ task calc_tpm {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 1
     }
 }
diff --git a/tools/md5sum.wdl b/tools/md5sum.wdl
index dd8a2a5c..912c157f 100755
--- a/tools/md5sum.wdl
+++ b/tools/md5sum.wdl
@@ -36,7 +36,7 @@ task compute_checksum {
     runtime {
         memory: "4 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 1
     }
 }
diff --git a/tools/star.wdl b/tools/star.wdl
index b088263c..99b25ff8 100755
--- a/tools/star.wdl
+++ b/tools/star.wdl
@@ -127,7 +127,7 @@ task build_star_db {
         cpu: ncpu
         memory: "~{memory_gb} GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/star:2.7.11b-5"
+        container: "ghcr.io/stjudecloud/star:branch-update_images-2.7.11b-5"
         maxRetries: 1
     }
 }
@@ -833,7 +833,7 @@ task alignment {
         cpu: ncpu
         memory: "50 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/star:2.7.11b-5"
+        container: "ghcr.io/stjudecloud/star:branch-update_images-2.7.11b-5"
         maxRetries: 1
     }
 }
diff --git a/tools/util.wdl b/tools/util.wdl
index 4948de58..67bf828a 100644
--- a/tools/util.wdl
+++ b/tools/util.wdl
@@ -42,7 +42,7 @@ task download {
     runtime {
         memory: "4 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 1
     }
 }
@@ -139,7 +139,7 @@ task split_string {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 1
     }
 }
@@ -363,7 +363,7 @@ task unpack_tarball {
     runtime {
         memory: "4 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 1
     }
 }
@@ -683,7 +683,7 @@ task global_phred_scores {
     runtime {
         memory: "4 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 1
     }
 }
@@ -761,7 +761,7 @@ task qc_summary {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 1
     }
 }
@@ -822,7 +822,7 @@ task split_fastq {
         cpu: ncpu
         memory: "4 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 1
     }
 }
diff --git a/workflows/dnaseq/dnaseq-standard-fastq.wdl b/workflows/dnaseq/dnaseq-standard-fastq.wdl
index 26e88c47..40d97f15 100644
--- a/workflows/dnaseq/dnaseq-standard-fastq.wdl
+++ b/workflows/dnaseq/dnaseq-standard-fastq.wdl
@@ -159,7 +159,7 @@ task parse_input {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 0
     }
 }
diff --git a/workflows/dnaseq/dnaseq-standard.wdl b/workflows/dnaseq/dnaseq-standard.wdl
index 5e39d9c6..abda03a0 100644
--- a/workflows/dnaseq/dnaseq-standard.wdl
+++ b/workflows/dnaseq/dnaseq-standard.wdl
@@ -136,7 +136,7 @@ task parse_input {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 0
     }
 }
diff --git a/workflows/methylation/methylation-cohort.wdl b/workflows/methylation/methylation-cohort.wdl
index f6198dbc..1b1bb173 100644
--- a/workflows/methylation/methylation-cohort.wdl
+++ b/workflows/methylation/methylation-cohort.wdl
@@ -124,7 +124,7 @@ task combine_data {
     }
 
     runtime {
-        container: "ghcr.io/stjudecloud/pandas:2.2.1-3"
+        container: "ghcr.io/stjudecloud/pandas:branch-update_images-2.2.1-3"
         memory: "~{memory_gb} GB"
         cpu: 1
         disks: "~{disk_size_gb} GB"
@@ -170,7 +170,7 @@ task filter_probes {
     }
 
     runtime {
-        container: "ghcr.io/stjudecloud/pandas:2.2.1-3"
+        container: "ghcr.io/stjudecloud/pandas:branch-update_images-2.2.1-3"
         memory: "8 GB"
         cpu: 1
         disks: "~{disk_size_gb} GB"
@@ -199,7 +199,7 @@ task generate_umap {
     Int disk_size_gb = ceil(size(filtered_beta_values, "GiB") * 2) + 2
 
     command <<<
-        python $(which generate_umap.py) \
+        python /usr/local/bin/generate_umap.py \
             --beta ~{filtered_beta_values} \
             --output-name ~{prefix}.csv
     >>>
@@ -209,7 +209,7 @@ task generate_umap {
     }
 
     runtime {
-        container: "ghcr.io/stjudecloud/umap:0.5.7-3"
+        container: "ghcr.io/stjudecloud/umap:branch-update_images-0.5.7-4"
         memory: "8 GB"
         cpu: 1
         disks: "~{disk_size_gb} GB"
@@ -236,7 +236,7 @@ task plot_umap {
     }
 
     command <<<
-        python $(which plot_umap.py) --umap ~{umap} --output-name ~{plot_file}
+        python /usr/local/bin/plot_umap.py --umap ~{umap} --output-name ~{plot_file}
     >>>
 
     output {
@@ -244,7 +244,7 @@ task plot_umap {
     }
 
     runtime {
-        container: "ghcr.io/stjudecloud/python-plotting:1.2.1"
+        container: "ghcr.io/stjudecloud/python-plotting:branch-update_images-2.0.0"
         memory: "4 GB"
         cpu: 1
         disks: "4 GB"
diff --git a/workflows/methylation/methylation-preprocess.wdl b/workflows/methylation/methylation-preprocess.wdl
index 9d0477a9..6f08920f 100644
--- a/workflows/methylation/methylation-preprocess.wdl
+++ b/workflows/methylation/methylation-preprocess.wdl
@@ -53,7 +53,7 @@ task process_raw_idats {
     }
 
     runtime {
-        container: "ghcr.io/stjudecloud/minfi:1.48.0-2"
+        container: "ghcr.io/stjudecloud/minfi:branch-update_images-1.48.0-2"
         memory: "8 GB"
         cpu: 1
         disks: "~{disk_size_gb} GB"
diff --git a/workflows/qc/quality-check-standard.wdl b/workflows/qc/quality-check-standard.wdl
index 4bb01a97..61d37f71 100644
--- a/workflows/qc/quality-check-standard.wdl
+++ b/workflows/qc/quality-check-standard.wdl
@@ -557,7 +557,7 @@ task parse_input {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 1
     }
 }
diff --git a/workflows/rnaseq/rnaseq-standard.wdl b/workflows/rnaseq/rnaseq-standard.wdl
index ae87e045..bc1bade4 100755
--- a/workflows/rnaseq/rnaseq-standard.wdl
+++ b/workflows/rnaseq/rnaseq-standard.wdl
@@ -179,7 +179,7 @@ task parse_input {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:1.5.1"
+        container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0"
         maxRetries: 1
     }
 }