broadinstitute · jessicaway · May 29, 2026 · Jun 2, 2026 · Jun 3, 2026 · Jun 3, 2026
diff --git a/.gitignore b/.gitignore
@@ -11,6 +11,7 @@ verification/test-wdls/__pycache__/
 
 # VSCode project settings
 .vscode
+warp.code-workspace
 
 # python virtual environments
 venv/

diff --git a/all_of_us/mitochondria/merge/mitochondria_merge.changelog.md b/all_of_us/mitochondria/merge/mitochondria_merge.changelog.md
@@ -17,13 +17,13 @@
 
 * Updated coverage HDF5 dtype from inferred uint16 to a fixed uint32 default to prevent silent truncation of high-coverage positions; added an explicit overflow guard that raises an error if any coverage value exceeds the dtype maximum
 
-aou_9.0.0
+# aou_9.0.0
 2026-03-23 (Date of Last Commit)
 
 * Version of the pipeline use to process AoU v9 data
 
 
-aou_9_beta
+# aou_9_beta
 2025-10-31 (Date of Last Commit)
 
 * Added support for optional subsetting of inputs using a Terra data table TSV

diff --git a/pipeline_versions.txt b/pipeline_versions.txt
@@ -12,22 +12,22 @@ IlluminaGenotypingArray	 1.12.27	2026-01-21
 Imputation	 1.1.23	2025-10-03 
 ImputationBeagle	 3.0.1	2026-02-23 
 JointGenotyping	 1.7.3	2025-08-11 
-MultiSampleSmartSeq2SingleNucleus	 2.2.7	2026-05-15 
-Multiome	 7.0.1	2026-05-15 
-Optimus	 9.1.0	2026-05-15 
-PairedTag	 3.0.1	2026-05-15 
+MultiSampleSmartSeq2SingleNucleus	 2.2.8	2026-06-03 
+Multiome	 7.0.2	2026-06-01 
+Optimus	 9.1.1	2026-06-01 
+PairedTag	 3.0.2	2026-06-03 
 PeakCalling	 1.0.1	2025-08-11 
 Pipeline Name	Version	Date of Last Commit
 RNAWithUMIsPipeline	 1.0.20	2026-01-21 
 ReblockGVCF	 2.4.4	2026-01-29 
-SlideSeq	 3.6.7	2026-05-15 
-SlideTags	 2.0.1	2026-05-15 
+SlideSeq	 3.6.8	2026-06-03 
+SlideTags	 2.0.2	2026-06-03 
 UltimaGenomicsJointGenotyping	 1.2.3	2025-08-11 
 UltimaGenomicsWholeGenomeCramOnly	 1.1.3	2026-01-21 
 UltimaGenomicsWholeGenomeGermline	 1.2.2	2026-01-29 
 VariantCalling	 2.2.8	2026-01-21 
 WholeGenomeGermlineSingleSample	 3.3.7	2026-01-21 
 WholeGenomeReprocessing	 3.3.7	2026-01-21 
-atac	 2.9.3	2025-09-19 
+atac	 2.9.4	2026-06-01 
 scANVI	 1.0.0	2026-04-17 
 snm3C	 4.1.1	2025-09-19 
diff --git a/pipelines/wdl/atac/atac.changelog.md b/pipelines/wdl/atac/atac.changelog.md
@@ -1,3 +1,9 @@
+# 2.9.4
+2026-06-01 (Date of Last Commit)
+
+* Added optional `input_id_name` input (default `"input_id"`) to allow callers to control the metadata key name under which `input_id` is stored in the ATAC h5ad `obs` columns and `uns` global attributes
+* Updated `warp-tools` docker tag to `2.7.1` (required for `--input_id_name` support)
+
 # 2.9.3
 2025-09-19 (Date of Last Commit)
 

diff --git a/pipelines/wdl/atac/atac.wdl b/pipelines/wdl/atac/atac.wdl
@@ -20,6 +20,8 @@ workflow ATAC {
 
     # Output prefix/base name for all intermediate files and pipeline outputs
     String input_id
+    # Key name used to label the input_id value in h5ad obs and uns metadata
+    String input_id_name = "input_id"
     String cloud_provider
     # Additional library aliquot ID
     String? atac_nhash_id
@@ -55,15 +57,15 @@ workflow ATAC {
     File? aligned_ATAC_bam
   }
 
-  String pipeline_version = "2.9.3"
+  String pipeline_version = "2.9.4"
 
   # Determine docker prefix based on cloud provider
   String gcr_docker_prefix = "us.gcr.io/broad-gotc-prod/"
   String acr_docker_prefix = "dsppipelinedev.azurecr.io/"
   String docker_prefix = if cloud_provider == "gcp" then gcr_docker_prefix else acr_docker_prefix
 
   # Docker image names
-  String warp_tools_docker = "warp-tools:2.6.1"
+  String warp_tools_docker = "warp-tools:2.7.1"
   String cutadapt_docker = "cutadapt:1.0.0-4.4-1686752919"
   String samtools_docker = "samtools-dist-bwa:3.0.0"
   String upstools_docker = "upstools:1.0.0-2023.03.03-1704300311"
@@ -153,7 +155,8 @@ workflow ATAC {
         docker_path = docker_prefix + snap_atac_docker,
         atac_nhash_id = atac_nhash_id,
         atac_expected_cells = atac_expected_cells,
-        input_id = input_id
+        input_id = input_id,
+        input_id_name = input_id_name
     }
   }
   if (!preindex) {
@@ -166,7 +169,8 @@ workflow ATAC {
         docker_path = docker_prefix + snap_atac_docker,
         atac_nhash_id = atac_nhash_id,
         atac_expected_cells = atac_expected_cells,
-        input_id = input_id
+        input_id = input_id,
+        input_id_name = input_id_name
     }
     if (peak_calling) {
       call peakcalling.PeakCalling as PeakCalling{
@@ -546,6 +550,7 @@ task CreateFragmentFile {
     String docker_path
     String atac_nhash_id = ""
     String input_id
+    String input_id_name = "input_id"
     Int atac_expected_cells = 3000
     String gtf_path = annotations_gtf
   }
@@ -578,6 +583,7 @@ task CreateFragmentFile {
     # set parameters
     bam = "~{bam}"
     input_id = "~{input_id}"
+    input_id_name = "~{input_id_name}"
     chrom_sizes = "~{chrom_sizes}"
     atac_gtf = "~{annotations_gtf}"
     preindex = "~{preindex}"
@@ -636,6 +642,9 @@ task CreateFragmentFile {
     atac_data = ad.read_h5ad("temp_metrics.h5ad")
     # Add nhash_id to h5ad file as unstructured metadata
     atac_data.uns['NHashID'] = atac_nhash_id
+    # Add input_id to obs (per-cell) and uns using the configurable key name
+    atac_data.obs[input_id_name] = input_id
+    atac_data.uns[input_id_name] = input_id
 
     # Add GTF to uns field
     # Original path from args.annotation_file

diff --git a/pipelines/wdl/multiome/Multiome.changelog.md b/pipelines/wdl/multiome/Multiome.changelog.md
@@ -1,3 +1,8 @@
+# 7.0.2
+2026-06-01 (Date of Last Commit)
+
+* Added optional `input_id_name` input (default `"input_id"`) threaded through to both Optimus (GEX) and ATAC sub-workflows, allowing callers to control the metadata key name under which `input_id` is stored in the h5ad outputs
+
 # 7.0.1
 2026-05-15 (Date of Last Commit)
 

diff --git a/pipelines/wdl/multiome/Multiome.wdl b/pipelines/wdl/multiome/Multiome.wdl
@@ -9,11 +9,13 @@ import "../../../tasks/wdl/Utilities.wdl" as utils
 
 workflow Multiome {
 
-    String pipeline_version = "7.0.1"
+    String pipeline_version = "7.0.2"
 
     input {
         String cloud_provider
         String input_id
+        # Key name used to label the input_id value in h5ad obs and uns metadata
+        String input_id_name = "input_id"
         # Additional library aliquot ID
         String? gex_nhash_id
         String? atac_nhash_id
@@ -93,6 +95,7 @@ workflow Multiome {
             r2_fastq = gex_r2_fastq,
             i1_fastq = gex_i1_fastq,
             input_id = input_id + "_gex",
+            input_id_name = input_id_name,
             output_bam_basename = input_id + "_gex",
             gex_nhash_id = gex_nhash_id,
             tar_star_reference = tar_star_reference,
@@ -105,7 +108,6 @@ workflow Multiome {
             ignore_r1_read_length = ignore_r1_read_length,
             star_strand_mode = star_strand_mode,
             soloMultiMappers = soloMultiMappers,
-            cloud_provider = cloud_provider,
             gex_expected_cells = expected_cells,
             run_cellbender = run_cellbender
     }
@@ -118,6 +120,7 @@ workflow Multiome {
             read2_fastq_gzipped = atac_r2_fastq,
             read3_fastq_gzipped = atac_r3_fastq,
             input_id = input_id + "_atac",
+            input_id_name = input_id_name,
             tar_bwa_reference = tar_bwa_reference,
             chrom_sizes = chrom_sizes,
             whitelist = atac_whitelist,

diff --git a/pipelines/wdl/optimus/Optimus.changelog.md b/pipelines/wdl/optimus/Optimus.changelog.md
@@ -1,3 +1,9 @@
+# 9.1.1
+2026-06-01 (Date of Last Commit)
+
+* Added optional `input_id_name` input (default `"input_id"`) to allow callers to control the metadata key name under which `input_id` is stored in the GEX h5ad `obs` columns and `uns` global attributes
+* Updated `warp-tools` docker tag to `2.7.1` (required for `--input_id_name` support)
+
 # 9.1.0
 2026-05-15 (Date of Last Commit)
 

diff --git a/pipelines/wdl/optimus/Optimus.wdl b/pipelines/wdl/optimus/Optimus.wdl
@@ -28,6 +28,8 @@ workflow Optimus {
     String input_id
     # String for additional library aliquot ID
     String? gex_nhash_id
+    # Key name used to label the input_id value in h5ad obs and uns metadata
+    String input_id_name = "input_id"
     String output_bam_basename = input_id
     String? input_name
     String? input_id_metadata_field
@@ -76,7 +78,7 @@ workflow Optimus {
   }
 
   # Version of this pipeline
-  String pipeline_version = "9.1.0"
+  String pipeline_version = "9.1.1"
 
   # this is used to scatter matched [r1_fastq, r2_fastq, i1_fastq] arrays
   Array[Int] indices = range(length(r1_fastq))
@@ -98,7 +100,7 @@ workflow Optimus {
   String pytools_docker = "pytools:1.0.0-1661263730"
   String empty_drops_docker = "empty-drops:1.0.1-4.2"
   String star_docker = "star:1.0.1-2.7.11a-1692706072"
-  String warp_tools_docker = "warp-tools:2.6.1"
+  String warp_tools_docker = "warp-tools:2.7.1"
   String star_merge_docker = "star-merge-npz:1.3.0"
   String samtools_star = "samtools-star:1.0.0-1.11-2.7.11a-1731516196"
   String samtools_star_python = "samtools-star-python:1.0.0"
@@ -117,6 +119,7 @@ workflow Optimus {
     r2_fastq: "reverse read, contains cDNA fragment generated from captured mRNA"
     i1_fastq: "index read used for demultiplexing; required when tenx_chemistry_version is 4"
     input_id: "name of sample matching this file, inserted into read group header"
+    input_id_name: "key name used to label the input_id value in h5ad obs and uns metadata (default: 'input_id')"
     input_id_metadata_field: "String that describes the metadata field containing the input_id"
     input_name: "User provided sample name or cell_names"
     input_name_metadata_field: "String that describes the metadata field containing the input_name"
@@ -215,6 +218,7 @@ workflow Optimus {
   call H5adUtils.OptimusH5adGeneration {
     input:
       input_id = input_id,
+      input_id_name = input_id_name,
       gex_nhash_id = gex_nhash_id,
       expected_cells = gex_expected_cells,
       input_name = input_name,

diff --git a/pipelines/wdl/paired_tag/PairedTag.changelog.md b/pipelines/wdl/paired_tag/PairedTag.changelog.md
@@ -1,3 +1,8 @@
+# 3.0.2
+2026-06-03 (Date of Last Commit)
+
+* Updated warp-tools docker to 2.7.1 (via Optimus sub-workflow); no functional impact on PairedTag outputs
+
 # 3.0.1
 2026-05-15 (Date of Last Commit)
 

diff --git a/pipelines/wdl/paired_tag/PairedTag.wdl b/pipelines/wdl/paired_tag/PairedTag.wdl
@@ -8,7 +8,7 @@ import "../../../tasks/wdl/Utilities.wdl" as utils
 
 workflow PairedTag {
 
-    String pipeline_version = "3.0.1"
+    String pipeline_version = "3.0.2"
 
     input {
         String input_id

diff --git a/pipelines/wdl/slideseq/SlideSeq.changelog.md b/pipelines/wdl/slideseq/SlideSeq.changelog.md
@@ -1,3 +1,8 @@
+# 3.6.8
+2026-06-03 (Date of Last Commit)
+
+* Updated warp-tools docker to 2.7.1 (via H5adUtils.wdl); no functional impact on SlideSeq outputs
+
 # 3.6.7
 2026-05-15 (Date of Last Commit)
 

diff --git a/pipelines/wdl/slideseq/SlideSeq.wdl b/pipelines/wdl/slideseq/SlideSeq.wdl
@@ -25,7 +25,7 @@ import "../../../tasks/wdl/Utilities.wdl" as utils
 
 workflow SlideSeq {
 
-    String pipeline_version = "3.6.7"
+    String pipeline_version = "3.6.8"
 
     input {
         Array[File] r1_fastq

diff --git a/pipelines/wdl/slidetags/SlideTags.changelog.md b/pipelines/wdl/slidetags/SlideTags.changelog.md
@@ -1,3 +1,8 @@
+# 2.0.2
+2026-06-03 (Date of Last Commit)
+
+* Updated warp-tools docker to 2.7.1 (via Optimus sub-workflow); no functional impact on SlideTags outputs
+
 # 2.0.1
 2026-05-15 (Date of Last Commit)
 

diff --git a/pipelines/wdl/slidetags/SlideTags.wdl b/pipelines/wdl/slidetags/SlideTags.wdl
@@ -6,7 +6,7 @@ import "../optimus/Optimus.wdl" as optimus
 
 workflow SlideTags {
 
-    String pipeline_version = "2.0.1"
+    String pipeline_version = "2.0.2"
 
     input {
 

diff --git a/...tseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md b/...tseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
@@ -1,3 +1,8 @@
+# 2.2.8
+2026-06-03 (Date of Last Commit)
+
+* Updated warp-tools docker to 2.7.1; no functional impact on MultiSampleSmartSeq2SingleNucleus outputs
+
 # 2.2.7
 2026-05-15 (Date of Last Commit)
 

diff --git a/pipelines/wdl/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl b/pipelines/wdl/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl
@@ -59,7 +59,7 @@ workflow MultiSampleSmartSeq2SingleNucleus {
   }
 
   # Version of this pipeline
-  String pipeline_version = "2.2.7"
+  String pipeline_version = "2.2.8"
 
   if (false) {
      String? none = "None"

diff --git a/tasks/wdl/H5adUtils.wdl b/tasks/wdl/H5adUtils.wdl
@@ -8,6 +8,7 @@ task OptimusH5adGeneration {
     String warp_tools_docker_path
     # name of the sample
     String input_id
+    String input_id_name = "input_id"
     String? gex_nhash_id
     # user provided id
     String counting_mode = "sc_rna"
@@ -71,6 +72,7 @@ task OptimusH5adGeneration {
           --gene_id  ~{gene_id} \
           --output_path_for_h5ad "~{input_id}" \
           --input_id ~{input_id} \
+          --input_id_name ~{input_id_name} \
           ~{"--input_name " + input_name} \
           ~{"--input_id_metadata_field " + input_id_metadata_field} \
           ~{"--input_name_metadata_field " + input_name_metadata_field} \
@@ -87,6 +89,7 @@ task OptimusH5adGeneration {
           --gene_id  ~{gene_id} \
           --output_path_for_h5ad "~{input_id}" \
           --input_id ~{input_id} \
+          --input_id_name ~{input_id_name} \
           ~{"--input_name " + input_name} \
           ~{"--input_id_metadata_field " + input_id_metadata_field} \
           ~{"--input_name_metadata_field " + input_name_metadata_field} \
@@ -143,6 +146,7 @@ task SingleNucleusOptimusH5adOutput {
         String warp_tools_docker_path
         # name of the sample
         String input_id
+        String input_id_name = "input_id"
         # additional aliquot id
         String? gex_nhash_id
         # user provided id
@@ -210,6 +214,7 @@ task SingleNucleusOptimusH5adOutput {
         --gene_id_2  ~{gene_id_exon} \
         --output_path_for_h5ad "~{input_id}" \
         --input_id ~{input_id} \
+        --input_id_name ~{input_id_name} \
         ~{"--input_name " + input_name} \
         ~{"--input_id_metadata_field " + input_id_metadata_field} \
         ~{"--input_name_metadata_field " + input_name_metadata_field} \
@@ -601,7 +606,7 @@ task SingleNucleusSlideseqH5adOutput {
 task SingleNucleusSmartSeq2H5adOutput {
     input {
         #runtime values
-        String docker = "us.gcr.io/broad-gotc-prod/warp-tools:2.6.1"
+        String docker = "us.gcr.io/broad-gotc-prod/warp-tools:2.7.1"
 
         Array[File] alignment_summary_metrics
         Array[File] dedup_metrics
@@ -696,7 +701,7 @@ task AggregateSmartSeq2H5ad {
         Array[File] h5ad_input
         String batch_id
         String pipeline_version
-        String docker = "us.gcr.io/broad-gotc-prod/warp-tools:2.6.1"
+        String docker = "us.gcr.io/broad-gotc-prod/warp-tools:2.7.1"
         Int disk = 200
         Int machine_mem_mb = 4000
         Int cpu = 1
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,6 +11,7 @@ verification/test-wdls/__pycache__/ @@
     # VSCode project settings
     .vscode
+    warp.code-workspace
     # python virtual environments
     venv/
@@ Expand Down @@