diff --git a/.github/workflows/warp_test_workflow.yml b/.github/workflows/warp_test_workflow.yml
index 8821240785..de4de52698 100644
--- a/.github/workflows/warp_test_workflow.yml
+++ b/.github/workflows/warp_test_workflow.yml
@@ -211,6 +211,7 @@ jobs:
           done
 
           echo "Error: The Dockstore Commit Hash does not match the GitHub Commit Hash after 15 minutes of retries!"
+          
           exit 1
         env:
           GITHUB_COMMIT_HASH: ${{ env.GITHUB_COMMIT_HASH }}
@@ -249,19 +250,18 @@ jobs:
           TEST_TYPE="${{ env.testType }}"
           INPUTS_DIR="${{ inputs.pipeline_dir }}/test_inputs/$TEST_TYPE"
           echo "Running tests with test type: $TEST_TYPE"
-
-          TRUTH_PATH="gs://broad-gotc-test-storage/${{ inputs.dockstore_pipeline_name }}/truth/$(echo "$TEST_TYPE" | tr '[:upper:]' '[:lower:]')/$TRUTH_BRANCH"
-          echo "Truth path: $TRUTH_PATH"
           
           RESULTS_PATH="gs://pd-test-results/${{ inputs.dockstore_pipeline_name }}/results/$CURRENT_TIME"
 
+
           # Submit all jobs first and store their submission IDs
           for input_file in "$INPUTS_DIR"/*.json; do
-            test_input_file=$(python3 scripts/firecloud_api/UpdateTestInputs.py --truth_path "$TRUTH_PATH" \
+            test_input_file=$(python3 scripts/firecloud_api/UpdateTestInputs.py \
                 --results_path "$RESULTS_PATH" \
                 --inputs_json "$input_file" \
                 --update_truth "$UPDATE_TRUTH_BOOL" \
-                --branch_name "$BRANCH_NAME" )
+                --branch_name "$TRUTH_BRANCH" \
+                --dockstore_pipeline_name "${{ inputs.dockstore_pipeline_name }}" )
             echo "Uploading the test input file: $test_input_file"
 
             # Create the submission_data.json file for this input_file
diff --git a/pipelines/broad/arrays/imputation/test_inputs/Plumbing/NA12878_trio.json b/pipelines/broad/arrays/imputation/test_inputs/Plumbing/NA12878_trio.json
index 2857a6f576..6830a61534 100644
--- a/pipelines/broad/arrays/imputation/test_inputs/Plumbing/NA12878_trio.json
+++ b/pipelines/broad/arrays/imputation/test_inputs/Plumbing/NA12878_trio.json
@@ -1,13 +1,13 @@
 {
   "Imputation.single_sample_vcfs": [
-    "gs://broad-gotc-test-storage/imputation/plumbing/vcfs/101342370027_R02C01.vcf.gz",
-    "gs://broad-gotc-test-storage/imputation/plumbing/vcfs/101342370027_R12C02.vcf.gz",
-    "gs://broad-gotc-test-storage/imputation/plumbing/vcfs/101342370134_R12C02.vcf.gz"
+    "gs://pd-test-storage-private/Imputation/input/plumbing/NA12878_trio/101342370027_R02C01.vcf.gz",
+    "gs://pd-test-storage-private/Imputation/input/plumbing/NA12878_trio/101342370027_R12C02.vcf.gz",
+    "gs://pd-test-storage-private/Imputation/input/plumbing/NA12878_trio/101342370134_R12C02.vcf.gz"
   ],
   "Imputation.single_sample_vcf_indices": [
-    "gs://broad-gotc-test-storage/imputation/plumbing/vcfs/101342370027_R02C01.vcf.gz.tbi",
-    "gs://broad-gotc-test-storage/imputation/plumbing/vcfs/101342370027_R12C02.vcf.gz.tbi",
-    "gs://broad-gotc-test-storage/imputation/plumbing/vcfs/101342370134_R12C02.vcf.gz.tbi"
+    "gs://pd-test-storage-private/Imputation/input/plumbing/NA12878_trio/101342370027_R02C01.vcf.gz.tbi",
+    "gs://pd-test-storage-private/Imputation/input/plumbing/NA12878_trio/101342370027_R12C02.vcf.gz.tbi",
+    "gs://pd-test-storage-private/Imputation/input/plumbing/NA12878_trio/101342370134_R12C02.vcf.gz.tbi"
   ],
   "Imputation.ref_dict": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict",
   "Imputation.reference_panel_path": "gs://gcp-public-data--broad-references/hg19/v0/1000G_reference_panel/",
diff --git a/pipelines/broad/arrays/imputation/test_inputs/Scientific/NA12878_trio_scientific.json b/pipelines/broad/arrays/imputation/test_inputs/Scientific/NA12878_trio_scientific.json
index 0596ac2577..1c844afce5 100644
--- a/pipelines/broad/arrays/imputation/test_inputs/Scientific/NA12878_trio_scientific.json
+++ b/pipelines/broad/arrays/imputation/test_inputs/Scientific/NA12878_trio_scientific.json
@@ -1,18 +1,18 @@
 {
   "Imputation.single_sample_vcfs": [
-    "gs://broad-gotc-test-storage/imputation/scientific/vcfs/101342370027_R02C01.vcf.gz",
-    "gs://broad-gotc-test-storage/imputation/scientific/vcfs/101342370027_R12C02.vcf.gz",
-    "gs://broad-gotc-test-storage/imputation/scientific/vcfs/101342370134_R12C02.vcf.gz"
+    "gs://pd-test-storage-private/Imputation/input/scientific/NA12878_trio_scientific/101342370027_R02C01.vcf.gz",
+    "gs://pd-test-storage-private/Imputation/input/scientific/NA12878_trio_scientific/101342370027_R12C02.vcf.gz",
+    "gs://pd-test-storage-private/Imputation/input/scientific/NA12878_trio_scientific/101342370134_R12C02.vcf.gz"
   ],
   "Imputation.single_sample_vcf_indices": [
-    "gs://broad-gotc-test-storage/imputation/scientific/vcfs/101342370027_R02C01.vcf.gz.tbi",
-    "gs://broad-gotc-test-storage/imputation/scientific/vcfs/101342370027_R12C02.vcf.gz.tbi",
-    "gs://broad-gotc-test-storage/imputation/scientific/vcfs/101342370134_R12C02.vcf.gz.tbi"
+    "gs://pd-test-storage-private/Imputation/input/scientific/NA12878_trio_scientific/101342370027_R02C01.vcf.gz.tbi",
+    "gs://pd-test-storage-private/Imputation/input/scientific/NA12878_trio_scientific/101342370027_R12C02.vcf.gz.tbi",
+    "gs://pd-test-storage-private/Imputation/input/scientific/NA12878_trio_scientific/101342370134_R12C02.vcf.gz.tbi"
   ],
   "Imputation.ref_dict": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict",
   "Imputation.reference_panel_path": "gs://gcp-public-data--broad-references/hg19/v0/1000G_reference_panel/",
   "Imputation.contigs": [ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22" ],
-  "Imputation.genetic_maps_eagle": "gs://broad-gotc-test-storage/imputation/eagle_genetic_map/genetic_map_hg19_withX.txt.gz",
+  "Imputation.genetic_maps_eagle": "gs://pd-test-storage-private/Imputation/input/scientific/NA12878_trio_scientific/genetic_map_hg19_withX.txt.gz",
   "Imputation.output_callset_name": "scientific_test",
   "Imputation.split_output_to_single_sample": false,
   "Imputation.perform_extra_qc_steps": false,
diff --git a/pipelines/broad/arrays/imputation/test_inputs/Scientific/multi_sample_split_test_data_NOT_PUBLIC.json b/pipelines/broad/arrays/imputation/test_inputs/Scientific/multi_sample_split_test_data_NOT_PUBLIC.json
index 08f855bfd1..1c3dea1836 100644
--- a/pipelines/broad/arrays/imputation/test_inputs/Scientific/multi_sample_split_test_data_NOT_PUBLIC.json
+++ b/pipelines/broad/arrays/imputation/test_inputs/Scientific/multi_sample_split_test_data_NOT_PUBLIC.json
@@ -1,6 +1,6 @@
 {
-  "Imputation.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation/scientific/vcfs/merged_input_samples.vcf.gz",
-  "Imputation.multi_sample_vcf_index": "gs://broad-gotc-test-storage/imputation/scientific/vcfs/merged_input_samples.vcf.gz.tbi",
+  "Imputation.multi_sample_vcf": "gs://pd-test-storage-private/Imputation/input/scientific/multi_sample_split_test_data_NOT_PUBLIC/merged_input_samples.vcf.gz",
+  "Imputation.multi_sample_vcf_index": "gs://pd-test-storage-private/Imputation/input/scientific/multi_sample_split_test_data_NOT_PUBLIC/merged_input_samples.vcf.gz.tbi",
   "Imputation.ref_dict": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict",
   "Imputation.reference_panel_path": "gs://gcp-public-data--broad-references/hg19/v0/1000G_reference_panel/",
   "Imputation.contigs": [ "21", "22" ],
diff --git a/pipelines/broad/arrays/imputation/test_inputs/Scientific/multi_sample_test_data_NOT_PUBLIC.json b/pipelines/broad/arrays/imputation/test_inputs/Scientific/multi_sample_test_data_NOT_PUBLIC.json
index ce7aa3e1af..64f6776810 100644
--- a/pipelines/broad/arrays/imputation/test_inputs/Scientific/multi_sample_test_data_NOT_PUBLIC.json
+++ b/pipelines/broad/arrays/imputation/test_inputs/Scientific/multi_sample_test_data_NOT_PUBLIC.json
@@ -1,6 +1,6 @@
 {
-  "Imputation.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation/scientific/vcfs/merged_input_samples.vcf.gz",
-  "Imputation.multi_sample_vcf_index": "gs://broad-gotc-test-storage/imputation/scientific/vcfs/merged_input_samples.vcf.gz.tbi",
+  "Imputation.multi_sample_vcf": "gs://pd-test-storage-private/Imputation/input/scientific/multi_sample_test_data_NOT_PUBLIC/merged_input_samples.vcf.gz",
+  "Imputation.multi_sample_vcf_index": "gs://pd-test-storage-private/Imputation/input/scientific/multi_sample_test_data_NOT_PUBLIC/merged_input_samples.vcf.gz.tbi",
   "Imputation.ref_dict": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict",
   "Imputation.reference_panel_path": "gs://gcp-public-data--broad-references/hg19/v0/1000G_reference_panel/",
   "Imputation.contigs": [ "21", "22" ],
diff --git a/pipelines/broad/arrays/imputation_beagle/test_inputs/Plumbing/NA12878_x10_hg38_arrays.json b/pipelines/broad/arrays/imputation_beagle/test_inputs/Plumbing/NA12878_x10_hg38_arrays.json
index bdf5a00597..fa9d0eef73 100644
--- a/pipelines/broad/arrays/imputation_beagle/test_inputs/Plumbing/NA12878_x10_hg38_arrays.json
+++ b/pipelines/broad/arrays/imputation_beagle/test_inputs/Plumbing/NA12878_x10_hg38_arrays.json
@@ -1,8 +1,8 @@
 {
-    "ImputationBeagle.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/scientific/vcfs/NA12878_10_duplicate.merged.cleaned.vcf.gz",
+    "ImputationBeagle.multi_sample_vcf": "gs://pd-test-storage-public/ImputationBeagle/input/plumbing/NA12878_x10_hg38_arrays/NA12878_10_duplicate.merged.cleaned.vcf.gz",
     "ImputationBeagle.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-    "ImputationBeagle.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+    "ImputationBeagle.reference_panel_path_prefix": "gs://pd-test-storage-public/ImputationBeagle/input/plumbing/NA12878_x10_hg38_arrays/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
     "ImputationBeagle.contigs": ["chr21","chr22"],
-    "ImputationBeagle.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ImputationBeagle.genetic_maps_path": "gs://pd-test-storage-public/ImputationBeagle/input/plumbing/NA12878_x10_hg38_arrays/plink-genetic-maps/",
     "ImputationBeagle.output_basename": "plumbing_test"
 }
diff --git a/pipelines/broad/arrays/imputation_beagle/test_inputs/Scientific/NA12878_x10_hg38_arrays.json b/pipelines/broad/arrays/imputation_beagle/test_inputs/Scientific/NA12878_x10_hg38_arrays.json
index 4263609e29..821b09dcf1 100644
--- a/pipelines/broad/arrays/imputation_beagle/test_inputs/Scientific/NA12878_x10_hg38_arrays.json
+++ b/pipelines/broad/arrays/imputation_beagle/test_inputs/Scientific/NA12878_x10_hg38_arrays.json
@@ -1,8 +1,8 @@
 {
-    "ImputationBeagle.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/scientific/vcfs/NA12878_10_duplicate.merged.cleaned.vcf.gz",
+    "ImputationBeagle.multi_sample_vcf": "gs://pd-test-storage-public/ImputationBeagle/input/scientific/NA12878_x10_hg38_arrays/NA12878_10_duplicate.merged.cleaned.vcf.gz",
     "ImputationBeagle.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-    "ImputationBeagle.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+    "ImputationBeagle.reference_panel_path_prefix": "gs://pd-test-storage-public/ImputationBeagle/input/scientific/NA12878_x10_hg38_arrays/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
     "ImputationBeagle.contigs": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
-    "ImputationBeagle.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ImputationBeagle.genetic_maps_path": "gs://pd-test-storage-public/ImputationBeagle/input/scientific/NA12878_x10_hg38_arrays/plink-genetic-maps/",
     "ImputationBeagle.output_basename": "scientific_test"
 }
diff --git a/pipelines/skylab/atac/test_inputs/Plumbing/10k_pbmc_downsampled.json b/pipelines/skylab/atac/test_inputs/Plumbing/10k_pbmc_downsampled.json
index 71be349541..f28014aef2 100644
--- a/pipelines/skylab/atac/test_inputs/Plumbing/10k_pbmc_downsampled.json
+++ b/pipelines/skylab/atac/test_inputs/Plumbing/10k_pbmc_downsampled.json
@@ -2,13 +2,13 @@
 	"ATAC.input_id":"10k_PBMC_downsampled",
 	"ATAC.cloud_provider":"gcp",
 	"ATAC.read1_fastq_gzipped":[
-	  "gs://pd-test-storage-public/Multiome/input/plumbing/fastq_R1_atac.fastq.gz"
+	  "gs://pd-test-storage-public/atac/input/plumbing/10k_pbmc_downsampled/fastq_R1_atac.fastq.gz"
 	],
 	"ATAC.read2_fastq_gzipped":[
-	  "gs://pd-test-storage-public/Multiome/input/plumbing/fastq_R2_atac.fastq.gz"
+	  "gs://pd-test-storage-public/atac/input/plumbing/10k_pbmc_downsampled/fastq_R2_atac.fastq.gz"
 	],
 	"ATAC.read3_fastq_gzipped":[
-	  "gs://pd-test-storage-public/Multiome/input/plumbing/fastq_R3_atac.fastq.gz"
+	  "gs://pd-test-storage-public/atac/input/plumbing/10k_pbmc_downsampled/fastq_R3_atac.fastq.gz"
 	],
 	"ATAC.tar_bwa_reference":"gs://gcp-public-data--broad-references/hg38/v0/bwa/v2_2_1/bwa-mem2-2.2.1-Human-GENCODE-build-GRCh38.tar",
 	"ATAC.chrom_sizes":"gs://pd-test-storage-public/Multiome/input/hg38.chrom.sizes",
diff --git a/pipelines/skylab/atac/test_inputs/Plumbing/8k_cortex.json b/pipelines/skylab/atac/test_inputs/Plumbing/8k_cortex.json
index d4a1858e72..cdf9e24394 100644
--- a/pipelines/skylab/atac/test_inputs/Plumbing/8k_cortex.json
+++ b/pipelines/skylab/atac/test_inputs/Plumbing/8k_cortex.json
@@ -2,13 +2,13 @@
 	"ATAC.input_id":"10x_8k_cortex_downsampled",
 	"ATAC.cloud_provider":"gcp",
 	"ATAC.read1_fastq_gzipped":[
-	  "gs://pd-test-storage-public/atac/input/plumbing/fastq_R1_0.fastq.gz"
+	  "gs://pd-test-storage-public/atac/input/plumbing/8k_cortex/fastq_R1_0.fastq.gz"
 	],
 	"ATAC.read2_fastq_gzipped":[
-	  "gs://pd-test-storage-public/atac/input/plumbing/fastq_R2_0.fastq.gz"
+	  "gs://pd-test-storage-public/atac/input/plumbing/8k_cortex/fastq_R2_0.fastq.gz"
 	],
 	"ATAC.read3_fastq_gzipped":[
-	  "gs://pd-test-storage-public/atac/input/plumbing/fastq_R3_0.fastq.gz"
+	  "gs://pd-test-storage-public/atac/input/plumbing/8k_cortex/fastq_R3_0.fastq.gz"
 	],
 	"ATAC.tar_bwa_reference":"gs://gcp-public-data--broad-references/GRCm39/bwa/v2_2_1/bwa-mem2-2.2.1-Mouse-GENCODE-build-GRCm39.tar",
 	"ATAC.chrom_sizes":"gs://gcp-public-data--broad-references/GRCm39/bwa/v2_2_1/chrom.sizes",
@@ -17,7 +17,7 @@
 	"ATAC.mem_size_bwa":"64", 
 	"ATAC.atac_nhash_id":"example_1234",
 	"ATAC.annotations_gtf":" gs://gcp-public-data--broad-references/GRCm39/star/v2_7_10a/modified_vM32.annotation.gtf",
-	"ATAC.whitelist":"gs://pd-test-storage-public/atac/input/plumbing/737K-cratac-v1.txt",
+	"ATAC.whitelist":"gs://pd-test-storage-public/atac/input/plumbing/8k_cortex/737K-cratac-v1.txt",
 	"ATAC.vm_size":"Standard_M128s",
 	"ATAC.peak_calling":true,
     "ATAC.PeakCalling.probability_threshold":"1.0",
diff --git a/pipelines/skylab/optimus/test_inputs/Scientific/inputs_8k_pbmc.json b/pipelines/skylab/optimus/test_inputs/Scientific/inputs_8k_pbmc.json
index 466716fdf8..628988194b 100644
--- a/pipelines/skylab/optimus/test_inputs/Scientific/inputs_8k_pbmc.json
+++ b/pipelines/skylab/optimus/test_inputs/Scientific/inputs_8k_pbmc.json
@@ -1,15 +1,15 @@
 {
   "Optimus.r1_fastq": [
-"gs://broad-gotc-test-storage/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L007_R1_001.fastq.gz",
-"gs://broad-gotc-test-storage/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L008_R1_001.fastq.gz"
+"gs://pd-test-storage-private/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L007_R1_001.fastq.gz",
+"gs://pd-test-storage-private/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L008_R1_001.fastq.gz"
   ],
   "Optimus.r2_fastq": [
-"gs://broad-gotc-test-storage/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L007_R2_001.fastq.gz",
-"gs://broad-gotc-test-storage/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L008_R2_001.fastq.gz"
+"gs://pd-test-storage-private/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L007_R2_001.fastq.gz",
+"gs://pd-test-storage-private/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L008_R2_001.fastq.gz"
   ],
   "Optimus.i1_fastq": [
-"gs://broad-gotc-test-storage/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L007_I1_001.fastq.gz",
-"gs://broad-gotc-test-storage/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L008_I1_001.fastq.gz"
+"gs://pd-test-storage-private/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L007_I1_001.fastq.gz",
+"gs://pd-test-storage-private/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L008_I1_001.fastq.gz"
   ],
   "Optimus.tar_star_reference": "gs://gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_star2.7.10a-Human-GENCODE-build-GRCh38-43.tar",
   "Optimus.input_id": "8k_pbmc",
diff --git a/pipelines/skylab/optimus/test_inputs/Scientific/inputs_8k_pbmc_stranded.json b/pipelines/skylab/optimus/test_inputs/Scientific/inputs_8k_pbmc_stranded.json
index 0a9ee3adc2..de2e17b569 100644
--- a/pipelines/skylab/optimus/test_inputs/Scientific/inputs_8k_pbmc_stranded.json
+++ b/pipelines/skylab/optimus/test_inputs/Scientific/inputs_8k_pbmc_stranded.json
@@ -1,15 +1,15 @@
 {
   "Optimus.r1_fastq": [
-"gs://broad-gotc-test-storage/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L007_R1_001.fastq.gz",
-"gs://broad-gotc-test-storage/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L008_R1_001.fastq.gz"
+"gs://pd-test-storage-private/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L007_R1_001.fastq.gz",
+"gs://pd-test-storage-private/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L008_R1_001.fastq.gz"
   ],
   "Optimus.r2_fastq": [
-"gs://broad-gotc-test-storage/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L007_R2_001.fastq.gz",
-"gs://broad-gotc-test-storage/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L008_R2_001.fastq.gz"
+"gs://pd-test-storage-private/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L007_R2_001.fastq.gz",
+"gs://pd-test-storage-private/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L008_R2_001.fastq.gz"
   ],
   "Optimus.i1_fastq": [
-"gs://broad-gotc-test-storage/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L007_I1_001.fastq.gz",
-"gs://broad-gotc-test-storage/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L008_I1_001.fastq.gz"
+"gs://pd-test-storage-private/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L007_I1_001.fastq.gz",
+"gs://pd-test-storage-private/Optimus/input/scientific/chemistry_X10_V2/8k_pbmc/fastqs/pbmc8k_S1_L008_I1_001.fastq.gz"
   ],
   "Optimus.tar_star_reference": "gs://gcp-public-data--broad-references/hg38/v0/star/star_2.7.9a_primary_gencode_human_v27.tar",
   "Optimus.input_id": "8k_pbmc",
diff --git a/pipelines/skylab/paired_tag/test_inputs/Plumbing/10k_pbmc_downsampled.json b/pipelines/skylab/paired_tag/test_inputs/Plumbing/10k_pbmc_downsampled.json
index cc083e1d9a..d58ae44f9e 100644
--- a/pipelines/skylab/paired_tag/test_inputs/Plumbing/10k_pbmc_downsampled.json
+++ b/pipelines/skylab/paired_tag/test_inputs/Plumbing/10k_pbmc_downsampled.json
@@ -2,23 +2,23 @@
   "PairedTag.annotations_gtf":"gs://gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf",
   "PairedTag.input_id":"10k_PBMC_downsampled",
   "PairedTag.gex_r1_fastq":[
-    "gs://pd-test-storage-public/Multiome/input/plumbing/fastq_R1_gex.fastq.gz"
+    "gs://pd-test-storage-public/PairedTag/input/plumbing/10k_PBMC_downsampled/fastq_R1_gex.fastq.gz"
   ],
   "PairedTag.gex_r2_fastq":[
-    "gs://pd-test-storage-public/Multiome/input/plumbing/fastq_R2_gex.fastq.gz"
+    "gs://pd-test-storage-public/PairedTag/input/plumbing/10k_PBMC_downsampled/fastq_R2_gex.fastq.gz"
   ],
   "PairedTag.atac_r1_fastq":[
-    "gs://pd-test-storage-public/Multiome/input/plumbing/fastq_R1_atac.fastq.gz"
+    "gs://pd-test-storage-public/PairedTag/input/plumbing/10k_PBMC_downsampled/fastq_R1_atac.fastq.gz"
   ],
   "PairedTag.atac_r2_fastq":[
-    "gs://pd-test-storage-public/Multiome/input/plumbing/fastq_R2_atac.fastq.gz"
+    "gs://pd-test-storage-public/PairedTag/input/plumbing/10k_PBMC_downsampled/fastq_R2_atac.fastq.gz"
   ],
   "PairedTag.atac_r3_fastq":[
-    "gs://pd-test-storage-public/Multiome/input/plumbing/fastq_R3_atac.fastq.gz"
+    "gs://pd-test-storage-public/PairedTag/input/plumbing/10k_PBMC_downsampled/fastq_R3_atac.fastq.gz"
   ],
   "PairedTag.tar_bwa_reference":"gs://gcp-public-data--broad-references/hg38/v0/bwa/v2_2_1/bwa-mem2-2.2.1-Human-GENCODE-build-GRCh38.tar",
   "PairedTag.tar_star_reference":"gs://gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_star2.7.10a-Human-GENCODE-build-GRCh38-43.tar",
-  "PairedTag.chrom_sizes":"gs://pd-test-storage-public/Multiome/input/hg38.chrom.sizes",
+  "PairedTag.chrom_sizes":"gs://pd-test-storage-public/PairedTag/input/hg38.chrom.sizes",
   "PairedTag.preindex":"false",
   "PairedTag.Atac_preindex.cpu_platform_bwa":"Intel Cascade Lake",
   "PairedTag.Atac_preindex.num_threads_bwa":"16",
diff --git a/pipelines/skylab/paired_tag/test_inputs/Scientific/BC011_10kPBMC.json b/pipelines/skylab/paired_tag/test_inputs/Scientific/BC011_10kPBMC.json
index fd0183b5c5..90bfeae64e 100644
--- a/pipelines/skylab/paired_tag/test_inputs/Scientific/BC011_10kPBMC.json
+++ b/pipelines/skylab/paired_tag/test_inputs/Scientific/BC011_10kPBMC.json
@@ -14,13 +14,13 @@
     "gs://pd-test-storage-public/Multiome/input/scientific/10k_PBMC_Multiome/10k_PBMC_Multiome_nextgem_Chromium_Controller_gex_S1_L002_R2_001.fastq.gz"
   ],
   "PairedTag.atac_r1_fastq":[
-    "gs://pd-test-storage-public/PairedTag/input/scientific/BC011_S1_L001_R1_001.fastq.gz"
+    "gs://pd-test-storage-public/PairedTag/input/scientific/BC011_10kPBMC/BC011_S1_L001_R1_001.fastq.gz"
   ],
   "PairedTag.atac_r2_fastq":[
-    "gs://pd-test-storage-public/PairedTag/input/scientific/BC011_S1_L001_R2_001.fastq.gz"
+    "gs://pd-test-storage-public/PairedTag/input/scientific/BC011_10kPBMC/BC011_S1_L001_R2_001.fastq.gz"
   ],
   "PairedTag.atac_r3_fastq":[
-    "gs://pd-test-storage-public/PairedTag/input/scientific/BC011_S1_L001_R3_001.fastq.gz"
+    "gs://pd-test-storage-public/PairedTag/input/scientific/BC011_10kPBMC/BC011_S1_L001_R3_001.fastq.gz"
   ],
   "PairedTag.chrom_sizes":"gs://pd-test-storage-public/Multiome/input/hg38.chrom.sizes",
   "PairedTag.preindex":"true",
diff --git a/pipelines/skylab/slideseq/test_inputs/Plumbing/Puck_210817_11.mm10.json b/pipelines/skylab/slideseq/test_inputs/Plumbing/Puck_210817_11.mm10.json
index 035b22c58e..0263c76edf 100644
--- a/pipelines/skylab/slideseq/test_inputs/Plumbing/Puck_210817_11.mm10.json
+++ b/pipelines/skylab/slideseq/test_inputs/Plumbing/Puck_210817_11.mm10.json
@@ -1,18 +1,18 @@
 {
-  "SlideSeq.r1_fastq": ["gs://broad-gotc-test-storage/slide_seq/plumbing/truth/master/210817_Puck_210817_11.L001_sampled_down.R1",
-    "gs://broad-gotc-test-storage/slide_seq/plumbing/truth/master/210817_Puck_210817_11.L002_sampled_down.R1",
-    "gs://broad-gotc-test-storage/slide_seq/plumbing/truth/master/210817_Puck_210817_11.L003_sampled_down.R1",
-    "gs://broad-gotc-test-storage/slide_seq/plumbing/truth/master/210817_Puck_210817_11.L004_sampled_down.R1"],
-  "SlideSeq.r2_fastq": ["gs://broad-gotc-test-storage/slide_seq/plumbing/truth/master/210817_Puck_210817_11.L001_sampled_down.R2",
-    "gs://broad-gotc-test-storage/slide_seq/plumbing/truth/master/210817_Puck_210817_11.L002_sampled_down.R2",
-    "gs://broad-gotc-test-storage/slide_seq/plumbing/truth/master/210817_Puck_210817_11.L003_sampled_down.R2",
-    "gs://broad-gotc-test-storage/slide_seq/plumbing/truth/master/210817_Puck_210817_11.L004_sampled_down.R2"],
+  "SlideSeq.r1_fastq": ["gs://pd-test-storage-public/SlideSeq/input/plumbing/Puck_210817_11/210817_Puck_210817_11.L001_sampled_down.R1",
+    "gs://pd-test-storage-public/SlideSeq/input/plumbing/Puck_210817_11/210817_Puck_210817_11.L002_sampled_down.R1",
+    "gs://pd-test-storage-public/SlideSeq/input/plumbing/Puck_210817_11/210817_Puck_210817_11.L003_sampled_down.R1",
+    "gs://pd-test-storage-public/SlideSeq/input/plumbing/Puck_210817_11/210817_Puck_210817_11.L004_sampled_down.R1"],
+  "SlideSeq.r2_fastq": ["gs://pd-test-storage-public/SlideSeq/input/plumbing/Puck_210817_11/210817_Puck_210817_11.L001_sampled_down.R2",
+    "gs://pd-test-storage-public/SlideSeq/input/plumbing/Puck_210817_11/210817_Puck_210817_11.L002_sampled_down.R2",
+    "gs://pd-test-storage-public/SlideSeq/input/plumbing/Puck_210817_11/210817_Puck_210817_11.L003_sampled_down.R2",
+    "gs://pd-test-storage-public/SlideSeq/input/plumbing/Puck_210817_11/210817_Puck_210817_11.L004_sampled_down.R2"],
   "SlideSeq.read_structure": "8C18X6C9M1X",
   "SlideSeq.input_id": "Puck_210817_11",
   "SlideSeq.output_bam_basename": "Puck_210817_11",
   "SlideSeq.tar_star_reference": "gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/star/modified_star_2.7.9a_primary_gencode_mouse_vM23.tar",
   "SlideSeq.annotations_gtf": "gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/modified_gencode.vM23.primary_assembly.annotation.gtf",
   "SlideSeq.count_exons": true,
-  "SlideSeq.bead_locations": " gs://broad-gotc-test-storage/SlideSeq/inputs/plumbing/Puck_210817_11/Puck_210817_11.tsv",
+  "SlideSeq.bead_locations": "gs://pd-test-storage-public/SlideSeq/input/plumbing/Puck_210817_11/Puck_210817_11.tsv",
   "SlideSeq.cloud_provider": "gcp"
 }
\ No newline at end of file
diff --git a/pipelines/skylab/slideseq/test_inputs/Scientific/Puck_210817_11.mm10.json b/pipelines/skylab/slideseq/test_inputs/Scientific/Puck_210817_11.mm10.json
index 458c4412ed..bf0bde8f34 100644
--- a/pipelines/skylab/slideseq/test_inputs/Scientific/Puck_210817_11.mm10.json
+++ b/pipelines/skylab/slideseq/test_inputs/Scientific/Puck_210817_11.mm10.json
@@ -1,20 +1,20 @@
 {
   "SlideSeq.r1_fastq": [
-"gs://broad-gotc-test-storage/SlideSeq/inputs/scientific/Puck_210817_11/Puck_210817_11_L01_R1.fastq.gz",
-"gs://broad-gotc-test-storage/SlideSeq/inputs/scientific/Puck_210817_11/Puck_210817_11_L02_R1.fastq.gz",
-"gs://broad-gotc-test-storage/SlideSeq/inputs/scientific/Puck_210817_11/Puck_210817_11_L03_R1.fastq.gz",
-"gs://broad-gotc-test-storage/SlideSeq/inputs/scientific/Puck_210817_11/Puck_210817_11_L04_R1.fastq.gz"],
+"gs://pd-test-storage-public/SlideSeq/input/scientific/Puck_210817_11/Puck_210817_11_L01_R1.fastq.gz",
+"gs://pd-test-storage-public/SlideSeq/input/scientific/Puck_210817_11/Puck_210817_11_L02_R1.fastq.gz",
+"gs://pd-test-storage-public/SlideSeq/input/scientific/Puck_210817_11/Puck_210817_11_L03_R1.fastq.gz",
+"gs://pd-test-storage-public/SlideSeq/input/scientific/Puck_210817_11/Puck_210817_11_L04_R1.fastq.gz"],
 "SlideSeq.r2_fastq": [
-"gs://broad-gotc-test-storage/SlideSeq/inputs/scientific/Puck_210817_11/Puck_210817_11_L01_R2.fastq.gz",
-"gs://broad-gotc-test-storage/SlideSeq/inputs/scientific/Puck_210817_11/Puck_210817_11_L02_R2.fastq.gz",
-"gs://broad-gotc-test-storage/SlideSeq/inputs/scientific/Puck_210817_11/Puck_210817_11_L03_R2.fastq.gz",
-"gs://broad-gotc-test-storage/SlideSeq/inputs/scientific/Puck_210817_11/Puck_210817_11_L04_R2.fastq.gz"],
+"gs://pd-test-storage-public/SlideSeq/input/scientific/Puck_210817_11/Puck_210817_11_L01_R2.fastq.gz",
+"gs://pd-test-storage-public/SlideSeq/input/scientific/Puck_210817_11/Puck_210817_11_L02_R2.fastq.gz",
+"gs://pd-test-storage-public/SlideSeq/input/scientific/Puck_210817_11/Puck_210817_11_L03_R2.fastq.gz",
+"gs://pd-test-storage-public/SlideSeq/input/scientific/Puck_210817_11/Puck_210817_11_L04_R2.fastq.gz"],
   "SlideSeq.read_structure": "8C18X6C9M1X",
   "SlideSeq.input_id": "210817_Puck_210817_11",
   "SlideSeq.output_bam_basename": "210817_Puck_210817_11",
   "SlideSeq.tar_star_reference": "gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/star/modified_star_2.7.9a_primary_gencode_mouse_vM23.tar",
   "SlideSeq.annotations_gtf": "gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/modified_gencode.vM23.primary_assembly.annotation.gtf",
   "SlideSeq.count_exons": true,
-  "SlideSeq.bead_locations": "gs://broad-gotc-test-storage/SlideSeq/inputs/scientific/Puck_210817_11/Puck_210817_11.tsv",
+  "SlideSeq.bead_locations": "gs://pd-test-storage-public/SlideSeq/input/scientific/Puck_210817_11/Puck_210817_11.tsv",
   "SlideSeq.cloud_provider": "gcp"
 }
diff --git a/pipelines/skylab/smartseq2_single_nucleus_multisample/test_inputs/Plumbing/mouse_example.json b/pipelines/skylab/smartseq2_single_nucleus_multisample/test_inputs/Plumbing/mouse_example.json
index 587a4aa5e4..bff802dd22 100644
--- a/pipelines/skylab/smartseq2_single_nucleus_multisample/test_inputs/Plumbing/mouse_example.json
+++ b/pipelines/skylab/smartseq2_single_nucleus_multisample/test_inputs/Plumbing/mouse_example.json
@@ -2,16 +2,16 @@
   "MultiSampleSmartSeq2SingleNucleus.genome_ref_fasta": "gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/modified_mm10.primary_assembly.genome.fa",
   "MultiSampleSmartSeq2SingleNucleus.tar_star_reference": "gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/star/modified_star_2.7.9a_primary_gencode_mouse_vM23.tar",
   "MultiSampleSmartSeq2SingleNucleus.annotations_gtf": "gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/modified_gencode.vM23.primary_assembly.annotation.gtf",
-  "MultiSampleSmartSeq2SingleNucleus.adapter_list": "gs://broad-gotc-test-storage/MultiSampleSmartSeq2SingleNucleus/adapters/Illumina_adapters_list.fa",
+  "MultiSampleSmartSeq2SingleNucleus.adapter_list": "gs://pd-test-storage-public/Smartseq2_Single_Nucleus_Multisample/input/plumbing/SM-GE644/adapters/Illumina_adapters_list.fa",
   "MultiSampleSmartSeq2SingleNucleus.fastq1_input_files": [
-    "gs://broad-gotc-test-storage/Smartseq2_Single_Nucleus_Multisample/truth/plumbing/master/pr_test_truth/SM-GE644_S110_E1-50_GGAGCTAC-CTAAGCCT_R1.fastq.gz",
-    "gs://broad-gotc-test-storage/Smartseq2_Single_Nucleus_Multisample/truth/plumbing/master/pr_test_truth/SM-GE644_S117_E1-50_GCGTAGTA-AAGGAGTA_R1.fastq.gz",
-    "gs://broad-gotc-test-storage/Smartseq2_Single_Nucleus_Multisample/truth/plumbing/master/pr_test_truth/SM-GE644_S118_E1-50_GCGTAGTA-CTAAGCCT_R1.fastq.gz"
+    "gs://pd-test-storage-public/Smartseq2_Single_Nucleus_Multisample/input/plumbing/SM-GE644/SM-GE644_S110_E1-50_GGAGCTAC-CTAAGCCT_R1.fastq.gz",
+    "gs://pd-test-storage-public/Smartseq2_Single_Nucleus_Multisample/input/plumbing/SM-GE644/SM-GE644_S117_E1-50_GCGTAGTA-AAGGAGTA_R1.fastq.gz",
+    "gs://pd-test-storage-public/Smartseq2_Single_Nucleus_Multisample/input/plumbing/SM-GE644/SM-GE644_S118_E1-50_GCGTAGTA-CTAAGCCT_R1.fastq.gz"
   ],
   "MultiSampleSmartSeq2SingleNucleus.fastq2_input_files": [
-    "gs://broad-gotc-test-storage/Smartseq2_Single_Nucleus_Multisample/truth/plumbing/master/pr_test_truth/SM-GE644_S110_E1-50_GGAGCTAC-CTAAGCCT_R2.fastq.gz",
-    "gs://broad-gotc-test-storage/Smartseq2_Single_Nucleus_Multisample/truth/plumbing/master/pr_test_truth/SM-GE644_S117_E1-50_GCGTAGTA-AAGGAGTA_R2.fastq.gz",
-    "gs://broad-gotc-test-storage/Smartseq2_Single_Nucleus_Multisample/truth/plumbing/master/pr_test_truth/SM-GE644_S118_E1-50_GCGTAGTA-CTAAGCCT_R2.fastq.gz"
+    "gs://pd-test-storage-public/Smartseq2_Single_Nucleus_Multisample/input/plumbing/SM-GE644/SM-GE644_S110_E1-50_GGAGCTAC-CTAAGCCT_R2.fastq.gz",
+    "gs://pd-test-storage-public/Smartseq2_Single_Nucleus_Multisample/input/plumbing/SM-GE644/SM-GE644_S117_E1-50_GCGTAGTA-AAGGAGTA_R2.fastq.gz",
+    "gs://pd-test-storage-public/Smartseq2_Single_Nucleus_Multisample/input/plumbing/SM-GE644/SM-GE644_S118_E1-50_GCGTAGTA-CTAAGCCT_R2.fastq.gz"
   ],
   "MultiSampleSmartSeq2SingleNucleus.input_ids": [
     "SM-GE644_S110_E1-50_GGAGCTAC-CTAAGCCT",
diff --git a/pipelines/skylab/snm3C/test_inputs/Plumbing/miseq_M16_G13.json b/pipelines/skylab/snm3C/test_inputs/Plumbing/miseq_M16_G13.json
index 047314bea1..a35c153044 100644
--- a/pipelines/skylab/snm3C/test_inputs/Plumbing/miseq_M16_G13.json
+++ b/pipelines/skylab/snm3C/test_inputs/Plumbing/miseq_M16_G13.json
@@ -1,21 +1,21 @@
 {
   "snm3C.fastq_input_read1": [
-    "gs://broad-gotc-test-storage/snM3C/inputs/plumbing/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L001_R1_001_fastq_R1_0.fastq.gz",
-    "gs://broad-gotc-test-storage/snM3C/inputs/plumbing/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L002_R1_001_fastq_R1_0.fastq.gz",
-    "gs://broad-gotc-test-storage/snM3C/inputs/plumbing/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L003_R1_001_fastq_R1_0.fastq.gz",
-    "gs://broad-gotc-test-storage/snM3C/inputs/plumbing/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L004_R1_001_fastq_R1_0.fastq.gz"
+    "gs://pd-test-storage-public/snm3C-seq/input/plumbing/miseq_M16_G13/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L001_R1_001_fastq_R1_0.fastq.gz",
+    "gs://pd-test-storage-public/snm3C-seq/input/plumbing/miseq_M16_G13/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L002_R1_001_fastq_R1_0.fastq.gz",
+    "gs://pd-test-storage-public/snm3C-seq/input/plumbing/miseq_M16_G13/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L003_R1_001_fastq_R1_0.fastq.gz",
+    "gs://pd-test-storage-public/snm3C-seq/input/plumbing/miseq_M16_G13/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L004_R1_001_fastq_R1_0.fastq.gz"
   ],
   "snm3C.fastq_input_read2": [
-    "gs://broad-gotc-test-storage/snM3C/inputs/plumbing/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L001_R1_001_fastq_R2_0.fastq.gz",
-    "gs://broad-gotc-test-storage/snM3C/inputs/plumbing/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L002_R1_001_fastq_R2_0.fastq.gz",
-    "gs://broad-gotc-test-storage/snM3C/inputs/plumbing/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L003_R1_001_fastq_R2_0.fastq.gz",
-    "gs://broad-gotc-test-storage/snM3C/inputs/plumbing/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L004_R1_001_fastq_R2_0.fastq.gz"
+    "gs://pd-test-storage-public/snm3C-seq/input/plumbing/miseq_M16_G13/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L001_R1_001_fastq_R2_0.fastq.gz",
+    "gs://pd-test-storage-public/snm3C-seq/input/plumbing/miseq_M16_G13/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L002_R1_001_fastq_R2_0.fastq.gz",
+    "gs://pd-test-storage-public/snm3C-seq/input/plumbing/miseq_M16_G13/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L003_R1_001_fastq_R2_0.fastq.gz",
+    "gs://pd-test-storage-public/snm3C-seq/input/plumbing/miseq_M16_G13/230117-AD3C-hs-snm3C_seq-NovaSeq-pe-150-PB-AD3C_BA17_2027_P1-1-B11_S1_L004_R1_001_fastq_R2_0.fastq.gz"
   ],
-  "snm3C.random_primer_indexes": "gs://broad-gotc-test-storage/snM3C/inputs/plumbing/random_index_M16_G13.fa",
+  "snm3C.random_primer_indexes": "gs://pd-test-storage-public/snm3C-seq/input/plumbing/miseq_M16_G13/random_index_M16_G13.fa",
   "snm3C.plate_id": "AD3C_BA17_2027_P1-1-B11",
-  "snm3C.tarred_index_files":"gs://broad-gotc-test-storage/methylome/input/plumbing/index_files/hg38_index_files.tar.gz",
-  "snm3C.chromosome_sizes": "gs://broad-gotc-test-storage/methylome/input/plumbing/index_files/hg38.chrom.sizes",
-  "snm3C.genome_fa": "gs://broad-gotc-test-storage/methylome/input/plumbing/index_files/hg38.fa",
+  "snm3C.tarred_index_files":"gs://pd-test-storage-public/snm3C-seq/input/plumbing/miseq_M16_G13/index_files/hg38_index_files.tar.gz",
+  "snm3C.chromosome_sizes": "gs://pd-test-storage-public/snm3C-seq/input/plumbing/miseq_M16_G13/index_files/hg38.chrom.sizes",
+  "snm3C.genome_fa": "gs://pd-test-storage-public/snm3C-seq/input/plumbing/miseq_M16_G13/index_files/hg38.fa",
   "snm3C.Hisat_paired_end.cpu_platform" : "Intel Cascade Lake",
   "snm3C.Hisat_single_end.cpu_platform" : "Intel Cascade Lake",
   "snm3C.Merge_sort_analyze.cpu_platform" : "Intel Cascade Lake",
diff --git a/pipelines/skylab/snm3C/test_inputs/Scientific/novaseq_M16_G13.json b/pipelines/skylab/snm3C/test_inputs/Scientific/novaseq_M16_G13.json
index 14441d35ae..ca590c16b6 100644
--- a/pipelines/skylab/snm3C/test_inputs/Scientific/novaseq_M16_G13.json
+++ b/pipelines/skylab/snm3C/test_inputs/Scientific/novaseq_M16_G13.json
@@ -1,21 +1,21 @@
 {
   "snm3C.fastq_input_read1": [
-    "gs://broad-gotc-test-storage/snM3C/inputs/scientific/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L001_R1_001_fastq_R1_0.fastq.gz",
-    "gs://broad-gotc-test-storage/snM3C/inputs/scientific/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L002_R1_001_fastq_R1_0.fastq.gz",
-    "gs://broad-gotc-test-storage/snM3C/inputs/scientific/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L003_R1_001_fastq_R1_0.fastq.gz",
-    "gs://broad-gotc-test-storage/snM3C/inputs/scientific/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L004_R1_001_fastq_R1_0.fastq.gz"
+    "gs://pd-test-storage-private/snm3C-seq/input/scientific/novaseq_M16_G13/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L001_R1_001_fastq_R1_0.fastq.gz",
+    "gs://pd-test-storage-private/snm3C-seq/input/scientific/novaseq_M16_G13/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L002_R1_001_fastq_R1_0.fastq.gz",
+    "gs://pd-test-storage-private/snm3C-seq/input/scientific/novaseq_M16_G13/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L003_R1_001_fastq_R1_0.fastq.gz",
+    "gs://pd-test-storage-private/snm3C-seq/input/scientific/novaseq_M16_G13/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L004_R1_001_fastq_R1_0.fastq.gz"
   ],
   "snm3C.fastq_input_read2": [
-    "gs://broad-gotc-test-storage/snM3C/inputs/scientific/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L001_R1_001_fastq_R2_0.fastq.gz",
-    "gs://broad-gotc-test-storage/snM3C/inputs/scientific/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L002_R1_001_fastq_R2_0.fastq.gz",
-    "gs://broad-gotc-test-storage/snM3C/inputs/scientific/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L003_R1_001_fastq_R2_0.fastq.gz",
-    "gs://broad-gotc-test-storage/snM3C/inputs/scientific/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L004_R1_001_fastq_R2_0.fastq.gz"
+    "gs://pd-test-storage-private/snm3C-seq/input/scientific/novaseq_M16_G13/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L001_R1_001_fastq_R2_0.fastq.gz",
+    "gs://pd-test-storage-private/snm3C-seq/input/scientific/novaseq_M16_G13/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L002_R1_001_fastq_R2_0.fastq.gz",
+    "gs://pd-test-storage-private/snm3C-seq/input/scientific/novaseq_M16_G13/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L003_R1_001_fastq_R2_0.fastq.gz",
+    "gs://pd-test-storage-private/snm3C-seq/input/scientific/novaseq_M16_G13/230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3_S1_L004_R1_001_fastq_R2_0.fastq.gz"
   ],
-  "snm3C.random_primer_indexes": "gs://broad-gotc-test-storage/snM3C/inputs/plumbing/random_index_M16_G13.fa",
+  "snm3C.random_primer_indexes": "gs://pd-test-storage-private/snm3C-seq/input/scientific/novaseq_M16_G13/random_index_M16_G13.fa",
   "snm3C.plate_id": "230419-iN-hs-snm3C_seq-NovaSeq-pe-150-BW-iN230412_Entorhinal_Cortex_Adult_2115_R1_1-1-I3",
-  "snm3C.tarred_index_files":"gs://broad-gotc-test-storage/methylome/input/plumbing/index_files/hg38_index_files.tar.gz",
-  "snm3C.chromosome_sizes": "gs://broad-gotc-test-storage/methylome/input/plumbing/index_files/hg38.chrom.sizes",
-  "snm3C.genome_fa": "gs://broad-gotc-test-storage/methylome/input/plumbing/index_files/hg38.fa",
+  "snm3C.tarred_index_files":"gs://pd-test-storage-private/snm3C-seq/input/scientific/novaseq_M16_G13/index_files/hg38_index_files.tar.gz",
+  "snm3C.chromosome_sizes": "gs://pd-test-storage-private/snm3C-seq/input/scientific/novaseq_M16_G13/index_files/hg38.chrom.sizes",
+  "snm3C.genome_fa": "gs://pd-test-storage-private/snm3C-seq/input/scientific/novaseq_M16_G13/index_files/hg38.fa",
   "snm3C.Hisat_paired_end.cpu_platform" : "Intel Cascade Lake",
   "snm3C.Hisat_single_end.cpu_platform" : "Intel Cascade Lake",
   "snm3C.Merge_sort_analyze.cpu_platform" : "Intel Cascade Lake",
diff --git a/scripts/firecloud_api/UpdateTestInputs.py b/scripts/firecloud_api/UpdateTestInputs.py
index 1eb45d85e9..056efadf0f 100644
--- a/scripts/firecloud_api/UpdateTestInputs.py
+++ b/scripts/firecloud_api/UpdateTestInputs.py
@@ -11,7 +11,29 @@ def format_float(value):
         return str(Decimal(str(value)))
     return value
 
-def update_test_inputs(inputs_json, truth_path, results_path, update_truth, branch_name):
+def determine_bucket_from_inputs(test_inputs):
+    """
+    Determine whether inputs are from public or private bucket by examining the values.
+    Returns the appropriate bucket path.
+    """
+    # Bucket paths to check
+    public_bucket = "gs://pd-test-storage-public"
+    private_bucket = "gs://pd-test-storage-private"
+
+    # Convert inputs to a string for easier searching
+    inputs_str = json.dumps(test_inputs)
+
+    # Check if any value contains reference to public bucket
+    if public_bucket in inputs_str:
+        return public_bucket
+    # Check if any value contains reference to private bucket
+    elif private_bucket in inputs_str:
+        return private_bucket
+
+    # Default to private bucket if no match found
+    return private_bucket
+
+def update_test_inputs(inputs_json, results_path, update_truth, branch_name, dockstore_pipeline_name):
     with open(inputs_json, 'r') as file:
         test_inputs = json.load(file)
 
@@ -19,10 +41,34 @@ def update_test_inputs(inputs_json, truth_path, results_path, update_truth, bran
     sample_name = os.path.splitext(os.path.basename(inputs_json))[0]
 
     # Get the pipeline name from the test inputs JSON
-    pipeline_name = next(iter(test_inputs)).split('.')[0]
+    pipeline_name_from_test_inputs = next(iter(test_inputs)).split('.')[0]
 
     # Append "Test" in front of the pipeline name
-    test_name = f"Test{pipeline_name}"
+    test_name = f"Test{pipeline_name_from_test_inputs}"
+
+    # Determine the correct bucket based on the input data
+    bucket_path = determine_bucket_from_inputs(test_inputs)
+
+    # Get the test type from the sample name or infer from the inputs
+    if "plumbing" in sample_name.lower():
+        test_type = "plumbing"
+    elif "scientific" in sample_name.lower():
+        test_type = "scientific"
+    else:
+        # Try to infer from the inputs
+        inputs_str = json.dumps(test_inputs).lower()
+        if "plumbing" in inputs_str:
+            test_type = "plumbing"
+        elif "scientific" in inputs_str:
+            test_type = "scientific"
+        else:
+            # Default to plumbing if we can't determine
+            test_type = "plumbing"
+
+    # Create the truth and results paths based on the determined bucket
+    # Extract the pipeline name from the input JSON for creating the bucket path
+    dockstore_pipeline_name = dockstore_pipeline_name
+    truth_path = f"{bucket_path}/{dockstore_pipeline_name}/truth/{test_type}/{branch_name}"
 
     # Update all keys and ensure nested inputs are handled correctly
     updated_inputs = {}
@@ -35,7 +81,7 @@ def update_test_inputs(inputs_json, truth_path, results_path, update_truth, bran
 
         # For nested keys (more than two parts), append the original pipeline name with a `.`
         if len(key_parts) > 2:
-            key_parts[1] = f"{pipeline_name}.{key_parts[1]}"
+            key_parts[1] = f"{pipeline_name_from_test_inputs}.{key_parts[1]}"
 
         # Reconstruct the updated key
         new_key = '.'.join(key_parts)
@@ -77,22 +123,17 @@ def update_test_inputs(inputs_json, truth_path, results_path, update_truth, bran
 
 def main():
     description = """This script updates the test inputs JSON to work with the test wrapper WDL,
-    which runs the pipeline and verification"""
+    which runs the pipeline and verification. It now determines the appropriate bucket (public or private)
+    based on the input data locations."""
 
     parser = argparse.ArgumentParser(description=description)
 
-    parser.add_argument(
-        "--truth_path",
-        dest="truth_path",
-        required=True,
-        help="The base path where the truth data is stored",
-    )
-
     parser.add_argument(
         "--results_path",
         dest="results_path",
-        required=True,
-        help="The base path where the test data will be stored",
+        required=False,
+        default="gs://pd-test-results",
+        help="The base path where the test data will be stored (now determined dynamically based on input data)",
     )
 
     parser.add_argument(
@@ -117,12 +158,18 @@ def main():
         required=True,
         help="Branch name of the current pipeline run")
 
+    parser.add_argument(
+        "--dockstore_pipeline_name",
+        required=True,
+        help="The pipeline name from Dockstore",
+    )
+
     args = parser.parse_args()
     # convert the update_truth flag to a boolean
     update_truth_bool = args.update_truth.lower() == "true"
 
     # Update the test inputs to work with the test wrapper WDL
-    update_test_inputs(args.inputs_json, args.truth_path, args.results_path, update_truth_bool, args.branch_name)
+    update_test_inputs(args.inputs_json, args.results_path, update_truth_bool, args.branch_name, args.dockstore_pipeline_name)
 
 if __name__ == "__main__":
     main()
\ No newline at end of file
diff --git a/tasks/broad/TerraCopyFilesFromCloudToCloud.wdl b/tasks/broad/TerraCopyFilesFromCloudToCloud.wdl
index 66b6eb69a4..1860151bff 100644
--- a/tasks/broad/TerraCopyFilesFromCloudToCloud.wdl
+++ b/tasks/broad/TerraCopyFilesFromCloudToCloud.wdl
@@ -30,9 +30,9 @@ task TerraCopyFilesFromCloudToCloud {
     echo ~{default='no_contamination' contamination} > contamination
 
     if ! grep -q no_contamination contamination; then
-      gcloud storage cp -L cp.log contamination ~{destination_cloud_path}.contamination
+      gcloud storage cp --project=warp-pipeline-dev --billing-project=terra-f8e3de20 -L cp.log contamination ~{destination_cloud_path}.contamination
     fi
-    gcloud storage cp ~{sep=' ' files_to_copy} ~{destination_cloud_path}
+    gcloud storage cp --project=warp-pipeline-dev --billing-project=terra-f8e3de20 ~{sep=' ' files_to_copy} ~{destination_cloud_path}
   }
 
   output {