broadinstitute · nikellepetrillo · Mar 19, 2025 · Mar 19, 2025 · Mar 19, 2025 · Mar 19, 2025
diff --git 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
@@ -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
@@ -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/...oad/arrays/imputation/test_inputs/Scientific/multi_sample_split_test_data_NOT_PUBLIC.json b/...oad/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/...nes/broad/arrays/imputation/test_inputs/Scientific/multi_sample_test_data_NOT_PUBLIC.json b/...nes/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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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",