From e2fef9ff1a4a904b0c4efcefa5b8aa2d71ff275b Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Wed, 8 Jan 2025 13:06:35 -0500
Subject: [PATCH 01/17] testing h5adutils with new docker

---
 tasks/skylab/H5adUtils.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl
index af83a9e3f8..b54a8eaa17 100644
--- a/tasks/skylab/H5adUtils.wdl
+++ b/tasks/skylab/H5adUtils.wdl
@@ -106,7 +106,7 @@ task OptimusH5adGeneration {
   >>>
 
   runtime {
-    docker: warp_tools_docker_path
+    docker: "us.gcr.io/broad-gotc-prod/warp-tools:lk-PD-2814-add-gtf-h5ad"
     cpu: cpu  # note that only 1 thread is supported by pseudobam
     memory: "~{machine_mem_mb} MiB"
     disks: "local-disk ~{disk} HDD"

From 12b99ac2a9ef500333a75148d6b7f681fbef6387 Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Wed, 8 Jan 2025 14:21:01 -0500
Subject: [PATCH 02/17] added GTF file to adata_uns

---
 pipelines/skylab/atac/atac.wdl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl
index c0c748c042..024f2e8fe5 100644
--- a/pipelines/skylab/atac/atac.wdl
+++ b/pipelines/skylab/atac/atac.wdl
@@ -601,6 +601,8 @@ 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
+
+    atac_data.uns['GTF'] = str(atac_gtf)
     # calculate tsse metrics
     snap.metrics.tsse(atac_data, atac_gtf)
     # Write new atac file

From 87b73d544c06ab777f0f38dd4c9747995ac4c794 Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Wed, 8 Jan 2025 15:24:34 -0500
Subject: [PATCH 03/17] changing name of warp_tools_docker variable so be
 version agnostic

---
 pipelines/skylab/optimus/Optimus.wdl | 12 ++++++------
 tasks/skylab/H5adUtils.wdl           |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
index 37d28381e2..f9e8bbe815 100644
--- a/pipelines/skylab/optimus/Optimus.wdl
+++ b/pipelines/skylab/optimus/Optimus.wdl
@@ -94,7 +94,7 @@ 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_2_2_0 = "warp-tools:2.5.0"
+  String warp_tools_docker = "warp-tools:lk-PD-2814-add-gtf-h5ad"
   String star_merge_docker = "star-merge-npz:1.3.0"
   String samtools_star = "samtools-star:1.0.0-1.11-2.7.11a-1731516196"
 
@@ -171,7 +171,7 @@ workflow Optimus {
       chemistry = tenx_chemistry_version,
       sample_id = input_id,
       read_struct = read_struct,
-      warp_tools_docker_path = docker_prefix + warp_tools_docker_2_2_0
+      warp_tools_docker_path = docker_prefix + warp_tools_docker
   }
 
   scatter(idx in range(length(SplitFastq.fastq_R1_output_array))) {
@@ -203,7 +203,7 @@ workflow Optimus {
       mt_genes = mt_genes,
       original_gtf = annotations_gtf,
       input_id = input_id,
-      warp_tools_docker_path = docker_prefix + warp_tools_docker_2_2_0
+      warp_tools_docker_path = docker_prefix + warp_tools_docker
   }
 
   call Metrics.CalculateCellMetrics as CellMetrics {
@@ -212,7 +212,7 @@ workflow Optimus {
       mt_genes = mt_genes,
       original_gtf = annotations_gtf,
       input_id = input_id,
-      warp_tools_docker_path = docker_prefix + warp_tools_docker_2_2_0
+      warp_tools_docker_path = docker_prefix + warp_tools_docker
   }
 
   call StarAlign.MergeStarOutput as MergeStarOutputs {
@@ -261,7 +261,7 @@ workflow Optimus {
         empty_drops_result = RunEmptyDrops.empty_drops_result,
         counting_mode = counting_mode,
         pipeline_version = "Optimus_v~{pipeline_version}",
-        warp_tools_docker_path = docker_prefix + warp_tools_docker_2_2_0
+        warp_tools_docker_path = docker_prefix + warp_tools_docker
     }
   }
   if (count_exons  && counting_mode=="sn_rna") {
@@ -300,7 +300,7 @@ workflow Optimus {
         cell_id_exon = MergeStarOutputsExons.row_index,
         gene_id_exon = MergeStarOutputsExons.col_index,
         pipeline_version = "Optimus_v~{pipeline_version}",
-        warp_tools_docker_path = docker_prefix + warp_tools_docker_2_2_0
+        warp_tools_docker_path = docker_prefix + warp_tools_docker
     }
   }
 
diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl
index b54a8eaa17..5304e113f7 100644
--- a/tasks/skylab/H5adUtils.wdl
+++ b/tasks/skylab/H5adUtils.wdl
@@ -106,7 +106,7 @@ task OptimusH5adGeneration {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-gotc-prod/warp-tools:lk-PD-2814-add-gtf-h5ad"
+    docker: "warp_tools_docker_path"
     cpu: cpu  # note that only 1 thread is supported by pseudobam
     memory: "~{machine_mem_mb} MiB"
     disks: "local-disk ~{disk} HDD"

From 2fec7b82a1f632fe359adcb6dbcf2f0eb2bb063f Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Wed, 8 Jan 2025 18:30:52 -0500
Subject: [PATCH 04/17] removed quotes

---
 tasks/skylab/H5adUtils.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl
index 5304e113f7..af83a9e3f8 100644
--- a/tasks/skylab/H5adUtils.wdl
+++ b/tasks/skylab/H5adUtils.wdl
@@ -106,7 +106,7 @@ task OptimusH5adGeneration {
   >>>
 
   runtime {
-    docker: "warp_tools_docker_path"
+    docker: warp_tools_docker_path
     cpu: cpu  # note that only 1 thread is supported by pseudobam
     memory: "~{machine_mem_mb} MiB"
     disks: "local-disk ~{disk} HDD"

From 38d731ce72c6680b15dd32d4284278fee1fa48f3 Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Thu, 9 Jan 2025 14:18:55 -0500
Subject: [PATCH 05/17] testing all wdls with new warp-tools docker

---
 pipelines/skylab/atac/atac.wdl         |  4 ++--
 pipelines/skylab/slideseq/SlideSeq.wdl | 10 +++++-----
 tasks/skylab/FastqProcessing.wdl       |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl
index 024f2e8fe5..a829413458 100644
--- a/pipelines/skylab/atac/atac.wdl
+++ b/pipelines/skylab/atac/atac.wdl
@@ -57,7 +57,7 @@ workflow ATAC {
   String docker_prefix = if cloud_provider == "gcp" then gcr_docker_prefix else acr_docker_prefix
 
   # Docker image names
-  String warp_tools_2_2_0 = "warp-tools:2.5.0"
+  String warp_tools_docker = "warp-tools:lk-PD-2814-add-gtf-h5ad"
   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"
@@ -99,7 +99,7 @@ workflow ATAC {
       output_base_name = input_id,
       num_output_files = GetNumSplits.ranks_per_node_out,
       whitelist = whitelist,
-      docker_path = docker_prefix + warp_tools_2_2_0
+      docker_path = docker_prefix + warp_tools_docker
   }
 
   scatter(idx in range(length(SplitFastq.fastq_R1_output_array))) {
diff --git a/pipelines/skylab/slideseq/SlideSeq.wdl b/pipelines/skylab/slideseq/SlideSeq.wdl
index e43f07979c..408b62eeb1 100644
--- a/pipelines/skylab/slideseq/SlideSeq.wdl
+++ b/pipelines/skylab/slideseq/SlideSeq.wdl
@@ -48,7 +48,7 @@ workflow SlideSeq {
     # docker images
     String pytools_docker = "pytools:1.0.0-1661263730"
     String picard_cloud_docker = "picard-cloud:2.26.10"
-    String warp_tools_docker_2_2_0 = "warp-tools:2.5.0"
+    String warp_tools_docker = "warp-tools:lk-PD-2814-add-gtf-h5ad"
     String star_merge_docker = "star-merge-npz:1.3.0"
 
     String ubuntu_docker = "ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf"
@@ -124,7 +124,7 @@ workflow SlideSeq {
             bam_input = MergeBam.output_bam,
             original_gtf = annotations_gtf,
             input_id = input_id,
-            warp_tools_docker_path = docker_prefix + warp_tools_docker_2_2_0
+            warp_tools_docker_path = docker_prefix + warp_tools_docker
     }
     call Metrics.CalculateUMIsMetrics as UMIsMetrics {
         input:
@@ -138,7 +138,7 @@ workflow SlideSeq {
             bam_input = MergeBam.output_bam,
             original_gtf = annotations_gtf,
             input_id = input_id,
-            warp_tools_docker_path = docker_prefix + warp_tools_docker_2_2_0
+            warp_tools_docker_path = docker_prefix + warp_tools_docker
 
     }
 
@@ -162,7 +162,7 @@ workflow SlideSeq {
                 gene_id = MergeStarOutputs.col_index,
                 add_emptydrops_data = "no",
                 pipeline_version = "SlideSeq_v~{pipeline_version}",
-                warp_tools_docker_path = docker_prefix + warp_tools_docker_2_2_0
+                warp_tools_docker_path = docker_prefix + warp_tools_docker
 
         }
     }
@@ -188,7 +188,7 @@ workflow SlideSeq {
                 cell_id_exon = MergeStarOutputsExons.row_index,
                 gene_id_exon = MergeStarOutputsExons.col_index,
                 pipeline_version = "SlideSeq_v~{pipeline_version}",
-                warp_tools_docker_path = docker_prefix + warp_tools_docker_2_2_0
+                warp_tools_docker_path = docker_prefix + warp_tools_docker
         }
     }
 
diff --git a/tasks/skylab/FastqProcessing.wdl b/tasks/skylab/FastqProcessing.wdl
index 5263f53ef2..9a6b3ed101 100644
--- a/tasks/skylab/FastqProcessing.wdl
+++ b/tasks/skylab/FastqProcessing.wdl
@@ -138,7 +138,7 @@ task FastqProcessingSlidSeq {
 
 
     # Runtime attributes
-    String docker =  "us.gcr.io/broad-gotc-prod/warp-tools:2.5.0"
+    String docker =  "us.gcr.io/broad-gotc-prod/warp-tools:lk-PD-2814-add-gtf-h5ad"
     Int cpu = 16
     Int machine_mb = 40000
     Int disk = ceil(size(r1_fastq, "GiB")*3 + size(r2_fastq, "GiB")*3) + 50

From 13fbf2aec6a5d1f2d273f5b2d0dbb50b31adbd43 Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Fri, 10 Jan 2025 15:23:37 -0500
Subject: [PATCH 06/17] updated h5ad with gs:// path for reference_gtf_file

---
 pipelines/skylab/atac/atac.wdl | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl
index a829413458..e147a24a75 100644
--- a/pipelines/skylab/atac/atac.wdl
+++ b/pipelines/skylab/atac/atac.wdl
@@ -602,7 +602,19 @@ task CreateFragmentFile {
     # Add nhash_id to h5ad file as unstructured metadata
     atac_data.uns['NHashID'] = atac_nhash_id
 
-    atac_data.uns['GTF'] = str(atac_gtf)
+    # Add GTF to uns field
+    
+    # Original path from args.annotation_file
+    annotation_gtf = str(atac_gtf)  # e.g., '/cromwell_root/gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
+
+    # Transform the path
+    if annotation_gtf.startswith('/cromwell_root/'):
+        stripped_path = annotation_gtf[len('/cromwell_root/'):]  # Remove '/cromwell_root/'
+        updated_path = f'gs://{stripped_path}'  # Add 'gs://' prefix
+    else:
+        updated_path = str(atac_gtf)
+    
+    atac_data.uns["reference_gtf_file"] = updated_path
     # calculate tsse metrics
     snap.metrics.tsse(atac_data, atac_gtf)
     # Write new atac file

From 7b5cae51ea79e01f2411bcdc4c6a8c297ef96b14 Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Fri, 10 Jan 2025 15:41:01 -0500
Subject: [PATCH 07/17] testing gtf path

---
 pipelines/skylab/atac/atac.wdl | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl
index e147a24a75..437a87fa5f 100644
--- a/pipelines/skylab/atac/atac.wdl
+++ b/pipelines/skylab/atac/atac.wdl
@@ -605,16 +605,16 @@ task CreateFragmentFile {
     # Add GTF to uns field
     
     # Original path from args.annotation_file
-    annotation_gtf = str(atac_gtf)  # e.g., '/cromwell_root/gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
-
-    # Transform the path
-    if annotation_gtf.startswith('/cromwell_root/'):
-        stripped_path = annotation_gtf[len('/cromwell_root/'):]  # Remove '/cromwell_root/'
-        updated_path = f'gs://{stripped_path}'  # Add 'gs://' prefix
-    else:
-        updated_path = str(atac_gtf)
+    gtf_path = str(~{annotations_gtf})  # e.g., '/cromwell_root/gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
+
+    # # Transform the path
+    # if annotation_gtf.startswith('/cromwell_root/'):
+    #     stripped_path = annotation_gtf[len('/cromwell_root/'):]  # Remove '/cromwell_root/'
+    #     updated_path = f'gs://{stripped_path}'  # Add 'gs://' prefix
+    # else:
+    #     updated_path = str(atac_gtf)
     
-    atac_data.uns["reference_gtf_file"] = updated_path
+    atac_data.uns["reference_gtf_file"] = gtf_path
     # calculate tsse metrics
     snap.metrics.tsse(atac_data, atac_gtf)
     # Write new atac file

From cb69b95be3a868ef60c42cd6f657b78c2a5fff20 Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Fri, 10 Jan 2025 15:51:51 -0500
Subject: [PATCH 08/17] testing new script and new logging for gtf path

---
 tasks/skylab/H5adUtils.wdl | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl
index af83a9e3f8..1ac71225f2 100644
--- a/tasks/skylab/H5adUtils.wdl
+++ b/tasks/skylab/H5adUtils.wdl
@@ -57,6 +57,12 @@ task OptimusH5adGeneration {
 
     touch empty_drops_result.csv
 
+    # Save the path of the annotation_file to a variable
+    gtf_path="~{annotation_file}"
+
+    # Echo the gtf_path for logging/debugging purposes
+    echo "GTF Path: $gtf_path"
+
     if [ "~{counting_mode}" == "sc_rna" ]; then
         python3 /warptools/scripts/create_h5ad_optimus.py \
           ~{if defined(empty_drops_result) then "--empty_drops_file  " + empty_drops_result  else "--empty_drops_file empty_drops_result.csv "  } \
@@ -74,6 +80,7 @@ task OptimusH5adGeneration {
           --count_matrix ~{sparse_count_matrix} \
           --expression_data_type "exonic" \
           --pipeline_version ~{pipeline_version}
+          --gtf-path $gtf_path
     else
         python3 /warptools/scripts/create_snrna_optimus_full_h5ad.py \
           --annotation_file ~{annotation_file} \

From 6f10319727817f46fdffe1b3d4cf9a847881649d Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Fri, 10 Jan 2025 16:00:36 -0500
Subject: [PATCH 09/17] updated gtf_path

---
 tasks/skylab/H5adUtils.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl
index 1ac71225f2..f5bb418e91 100644
--- a/tasks/skylab/H5adUtils.wdl
+++ b/tasks/skylab/H5adUtils.wdl
@@ -80,7 +80,7 @@ task OptimusH5adGeneration {
           --count_matrix ~{sparse_count_matrix} \
           --expression_data_type "exonic" \
           --pipeline_version ~{pipeline_version}
-          --gtf-path $gtf_path
+          --gtf_path $gtf_path
     else
         python3 /warptools/scripts/create_snrna_optimus_full_h5ad.py \
           --annotation_file ~{annotation_file} \

From 422ad3be3a4f30383e41aa96767ca66bdb4013b1 Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Fri, 10 Jan 2025 20:01:53 -0500
Subject: [PATCH 10/17] testing fix for wdl gtf_path syntax

---
 pipelines/skylab/atac/atac.wdl | 3 ++-
 tasks/skylab/H5adUtils.wdl     | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl
index 437a87fa5f..92037920b8 100644
--- a/pipelines/skylab/atac/atac.wdl
+++ b/pipelines/skylab/atac/atac.wdl
@@ -521,6 +521,7 @@ task CreateFragmentFile {
     String atac_nhash_id = ""
     String input_id
     Int atac_expected_cells = 3000
+    String gtf_path = annotations_gtf
   }
 
   parameter_meta {
@@ -605,7 +606,7 @@ task CreateFragmentFile {
     # Add GTF to uns field
     
     # Original path from args.annotation_file
-    gtf_path = str(~{annotations_gtf})  # e.g., '/cromwell_root/gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
+    gtf_path = "~{gtf_path}"  # e.g., '/cromwell_root/gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
 
     # # Transform the path
     # if annotation_gtf.startswith('/cromwell_root/'):
diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl
index f5bb418e91..8d5b279c56 100644
--- a/tasks/skylab/H5adUtils.wdl
+++ b/tasks/skylab/H5adUtils.wdl
@@ -79,7 +79,7 @@ task OptimusH5adGeneration {
           ~{"--input_name_metadata_field " + input_name_metadata_field} \
           --count_matrix ~{sparse_count_matrix} \
           --expression_data_type "exonic" \
-          --pipeline_version ~{pipeline_version}
+          --pipeline_version ~{pipeline_version} \
           --gtf_path $gtf_path
     else
         python3 /warptools/scripts/create_snrna_optimus_full_h5ad.py \

From 29a37fc5d8bac4baad10f3df89e5ffb2d68c497d Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Mon, 13 Jan 2025 09:54:01 -0500
Subject: [PATCH 11/17] added annotation file as string to h5ad utils task

---
 tasks/skylab/H5adUtils.wdl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl
index 8d5b279c56..e6a04977b1 100644
--- a/tasks/skylab/H5adUtils.wdl
+++ b/tasks/skylab/H5adUtils.wdl
@@ -34,6 +34,7 @@ task OptimusH5adGeneration {
     File? empty_drops_result
     String counting_mode = "sc_rna"
     String add_emptydrops_data = "yes"
+    String gtf_path = annotation_file
 
 
     String pipeline_version
@@ -58,7 +59,7 @@ task OptimusH5adGeneration {
     touch empty_drops_result.csv
 
     # Save the path of the annotation_file to a variable
-    gtf_path="~{annotation_file}"
+    gtf_path="~{gtf_path}"
 
     # Echo the gtf_path for logging/debugging purposes
     echo "GTF Path: $gtf_path"

From ee6c5b753e93bea3bbc590fd8d9a4e017d28a0a0 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Mon, 13 Jan 2025 14:54:28 +0000
Subject: [PATCH 12/17] Updated pipeline_versions.txt with all pipeline version
 information

---
 pipeline_versions.txt | 56 +++++++++++++++++++++----------------------
 1 file changed, 28 insertions(+), 28 deletions(-)

diff --git a/pipeline_versions.txt b/pipeline_versions.txt
index b24084e5fe..45c3483d7c 100644
--- a/pipeline_versions.txt
+++ b/pipeline_versions.txt
@@ -1,40 +1,40 @@
 Pipeline Name	Version	Date of Last Commit
-CheckFingerprint	 1.0.22	2024-10-28 
-RNAWithUMIsPipeline	 1.0.18	2024-11-04 
-AnnotationFiltration	 1.2.7	2024-11-04 
-UltimaGenomicsWholeGenomeGermline	 1.1.3	2024-12-05 
-WholeGenomeGermlineSingleSample	 3.3.3	2024-11-04 
-ExomeGermlineSingleSample	 3.2.3	2024-11-04 
-JointGenotypingByChromosomePartTwo	 1.5.2	2024-11-04 
-JointGenotypingByChromosomePartOne	 1.5.2	2024-11-04 
+ExomeReprocessing	 3.3.3	2024-11-04 
+CramToUnmappedBams	 1.1.3	2024-08-02 
+WholeGenomeReprocessing	 3.3.3	2024-11-04 
+ExternalExomeReprocessing	 3.3.3	2024-11-04 
+ExternalWholeGenomeReprocessing	 2.3.3	2024-11-04 
+UltimaGenomicsJointGenotyping	 1.2.2	2024-11-04 
 ReblockGVCF	 2.4.0	2024-12-05 
+JointGenotypingByChromosomePartOne	 1.5.2	2024-11-04 
+JointGenotypingByChromosomePartTwo	 1.5.2	2024-11-04 
 JointGenotyping	 1.7.2	2024-11-04 
-UltimaGenomicsJointGenotyping	 1.2.2	2024-11-04 
+ExomeGermlineSingleSample	 3.2.3	2024-11-04 
+WholeGenomeGermlineSingleSample	 3.3.3	2024-11-04 
+UltimaGenomicsWholeGenomeGermline	 1.1.3	2024-12-05 
 VariantCalling	 2.2.4	2024-11-04 
-UltimaGenomicsWholeGenomeCramOnly	 1.0.23	2024-11-04 
 GDCWholeGenomeSomaticSingleSample	 1.3.4	2024-11-04 
-BroadInternalRNAWithUMIs	 1.0.36	2024-11-04 
-BroadInternalUltimaGenomics	 1.1.3	2024-12-05 
-BroadInternalArrays	 1.1.14	2024-11-04 
-BroadInternalImputation	 1.1.14	2024-11-04 
-Arrays	 2.6.30	2024-11-04 
+UltimaGenomicsWholeGenomeCramOnly	 1.0.23	2024-11-04 
+IlluminaGenotypingArray	 1.12.24	2024-11-04 
+AnnotationFiltration	 1.2.7	2024-11-04 
+CheckFingerprint	 1.0.22	2024-10-28 
 ValidateChip	 1.16.7	2024-11-04 
-MultiSampleArrays	 1.6.2	2024-08-02 
 Imputation	 1.1.15	2024-11-04 
-IlluminaGenotypingArray	 1.12.24	2024-11-04 
-ExternalWholeGenomeReprocessing	 2.3.3	2024-11-04 
-ExternalExomeReprocessing	 3.3.3	2024-11-04 
-CramToUnmappedBams	 1.1.3	2024-08-02 
-WholeGenomeReprocessing	 3.3.3	2024-11-04 
-ExomeReprocessing	 3.3.3	2024-11-04 
+MultiSampleArrays	 1.6.2	2024-08-02 
+Arrays	 2.6.30	2024-11-04 
+BroadInternalUltimaGenomics	 1.1.3	2024-12-05 
+BroadInternalImputation	 1.1.14	2024-11-04 
+BroadInternalArrays	 1.1.14	2024-11-04 
+BroadInternalRNAWithUMIs	 1.0.36	2024-11-04 
+RNAWithUMIsPipeline	 1.0.18	2024-11-04 
+Multiome	 5.9.4	2024-12-05 
+MultiSampleSmartSeq2SingleNucleus	 2.0.6	2024-11-15 
 BuildIndices	 3.1.0	2024-11-26 
+SlideSeq	 3.4.7	2024-12-3 
+PairedTag	 1.9.0	2024-12-05 
+atac	 2.5.3	2024-11-22 
 scATAC	 1.3.2	2023-08-03 
 snm3C	 4.0.4	2024-08-06 
-Multiome	 5.9.4	2024-12-05 
-PairedTag	 1.9.0	2024-12-05 
-MultiSampleSmartSeq2	 2.2.22	2024-09-11 
-MultiSampleSmartSeq2SingleNucleus	 2.0.6	2024-11-15 
 Optimus	 7.9.0	2024-12-05 
-atac	 2.5.3	2024-11-22 
+MultiSampleSmartSeq2	 2.2.22	2024-09-11 
 SmartSeq2SingleSample	 5.1.21	2024-09-11 
-SlideSeq	 3.4.7	2024-12-3 

From 4e74a75a0edbb38cc595a467f44a827d3ecb15b9 Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Mon, 13 Jan 2025 10:32:53 -0500
Subject: [PATCH 13/17] updating gtf_path for remaining scripts

---
 tasks/skylab/H5adUtils.wdl | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl
index e6a04977b1..dedd01a509 100644
--- a/tasks/skylab/H5adUtils.wdl
+++ b/tasks/skylab/H5adUtils.wdl
@@ -56,13 +56,7 @@ task OptimusH5adGeneration {
   command <<<
     set -euo pipefail
 
-    touch empty_drops_result.csv
-
-    # Save the path of the annotation_file to a variable
-    gtf_path="~{gtf_path}"
-
-    # Echo the gtf_path for logging/debugging purposes
-    echo "GTF Path: $gtf_path"
+    touch empty_drops_result.csvs
 
     if [ "~{counting_mode}" == "sc_rna" ]; then
         python3 /warptools/scripts/create_h5ad_optimus.py \
@@ -81,7 +75,7 @@ task OptimusH5adGeneration {
           --count_matrix ~{sparse_count_matrix} \
           --expression_data_type "exonic" \
           --pipeline_version ~{pipeline_version} \
-          --gtf_path $gtf_path
+          --gtf_path ~{gtf_path}
     else
         python3 /warptools/scripts/create_snrna_optimus_full_h5ad.py \
           --annotation_file ~{annotation_file} \
@@ -96,7 +90,8 @@ task OptimusH5adGeneration {
           ~{"--input_name_metadata_field " + input_name_metadata_field} \
           --count_matrix ~{sparse_count_matrix} \
           --expression_data_type "whole_transcript"\
-          --pipeline_version ~{pipeline_version}
+          --pipeline_version ~{pipeline_version} \
+          --gtf_path ~{gtf_path}
     fi
 
     # modify h5ad to include doublets, NHASHID, and build library metrics
@@ -166,6 +161,7 @@ task SingleNucleusOptimusH5adOutput {
         File? library_metrics
         # Cell calls from starsolo in TSV format
         File? cellbarcodes
+        String gtf_path = annotation_file
 
         String pipeline_version
 
@@ -202,7 +198,8 @@ task SingleNucleusOptimusH5adOutput {
         ~{"--input_id_metadata_field " + input_id_metadata_field} \
         ~{"--input_name_metadata_field " + input_name_metadata_field} \
         --expression_data_type "whole_transcript" \
-        --pipeline_version ~{pipeline_version}
+        --pipeline_version ~{pipeline_version} \
+        --gtf_path ~{gtf_path}
 
         # modify h5ad to include doublets, NHASHID, and build library metrics
         python3 /warptools/scripts/add_library_tso_doublets.py \

From e1ee33202067b038af1eb3c4ea3b279e13a8f541 Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Mon, 13 Jan 2025 15:01:50 -0500
Subject: [PATCH 14/17] updated warp-tools docker to versioned docker 2.6.0

---
 pipelines/skylab/atac/atac.wdl         | 2 +-
 pipelines/skylab/optimus/Optimus.wdl   | 2 +-
 pipelines/skylab/slideseq/SlideSeq.wdl | 2 +-
 tasks/skylab/FastqProcessing.wdl       | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl
index 92037920b8..c165b091b6 100644
--- a/pipelines/skylab/atac/atac.wdl
+++ b/pipelines/skylab/atac/atac.wdl
@@ -57,7 +57,7 @@ workflow ATAC {
   String docker_prefix = if cloud_provider == "gcp" then gcr_docker_prefix else acr_docker_prefix
 
   # Docker image names
-  String warp_tools_docker = "warp-tools:lk-PD-2814-add-gtf-h5ad"
+  String warp_tools_docker = "warp-tools:2.6.0"
   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"
diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
index f9e8bbe815..7031c1f676 100644
--- a/pipelines/skylab/optimus/Optimus.wdl
+++ b/pipelines/skylab/optimus/Optimus.wdl
@@ -94,7 +94,7 @@ 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:lk-PD-2814-add-gtf-h5ad"
+  String warp_tools_docker = "warp-tools:2.6.0"
   String star_merge_docker = "star-merge-npz:1.3.0"
   String samtools_star = "samtools-star:1.0.0-1.11-2.7.11a-1731516196"
 
diff --git a/pipelines/skylab/slideseq/SlideSeq.wdl b/pipelines/skylab/slideseq/SlideSeq.wdl
index 408b62eeb1..fdd9702393 100644
--- a/pipelines/skylab/slideseq/SlideSeq.wdl
+++ b/pipelines/skylab/slideseq/SlideSeq.wdl
@@ -48,7 +48,7 @@ workflow SlideSeq {
     # docker images
     String pytools_docker = "pytools:1.0.0-1661263730"
     String picard_cloud_docker = "picard-cloud:2.26.10"
-    String warp_tools_docker = "warp-tools:lk-PD-2814-add-gtf-h5ad"
+    String warp_tools_docker = "warp-tools:2.6.0"
     String star_merge_docker = "star-merge-npz:1.3.0"
 
     String ubuntu_docker = "ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf"
diff --git a/tasks/skylab/FastqProcessing.wdl b/tasks/skylab/FastqProcessing.wdl
index 9a6b3ed101..530eee652b 100644
--- a/tasks/skylab/FastqProcessing.wdl
+++ b/tasks/skylab/FastqProcessing.wdl
@@ -138,7 +138,7 @@ task FastqProcessingSlidSeq {
 
 
     # Runtime attributes
-    String docker =  "us.gcr.io/broad-gotc-prod/warp-tools:lk-PD-2814-add-gtf-h5ad"
+    String docker =  "us.gcr.io/broad-gotc-prod/warp-tools:2.6.0"
     Int cpu = 16
     Int machine_mb = 40000
     Int disk = ceil(size(r1_fastq, "GiB")*3 + size(r2_fastq, "GiB")*3) + 50

From 9b6b1904e21b5a9a8c8074e41cd65090efce78bf Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Mon, 13 Jan 2025 15:11:01 -0500
Subject: [PATCH 15/17] changelog updates

---
 pipelines/skylab/atac/atac.changelog.md                      | 5 +++++
 pipelines/skylab/atac/atac.wdl                               | 2 +-
 pipelines/skylab/multiome/Multiome.changelog.md              | 3 ++-
 pipelines/skylab/optimus/Optimus.changelog.md                | 4 +++-
 pipelines/skylab/paired_tag/PairedTag.changelog.md           | 5 +++--
 pipelines/skylab/slideseq/SlideSeq.changelog.md              | 3 ++-
 .../MultiSampleSmartSeq2SingleNucleus.changelog.md           | 3 ++-
 7 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/pipelines/skylab/atac/atac.changelog.md b/pipelines/skylab/atac/atac.changelog.md
index 578088a0d6..074e2e3614 100644
--- a/pipelines/skylab/atac/atac.changelog.md
+++ b/pipelines/skylab/atac/atac.changelog.md
@@ -1,3 +1,8 @@
+# 2.5.4
+2025-01-13 (Date of Last Commit)
+
+* Added reference_gtf_file to the output h5ad unstructured metadata
+
 # 2.5.3
 2024-11-22 (Date of Last Commit)
 
diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl
index c165b091b6..ddfc7c43a1 100644
--- a/pipelines/skylab/atac/atac.wdl
+++ b/pipelines/skylab/atac/atac.wdl
@@ -49,7 +49,7 @@ workflow ATAC {
     String adapter_seq_read3 = "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG"
   }
 
-  String pipeline_version = "2.5.3"
+  String pipeline_version = "2.5.4"
 
   # Determine docker prefix based on cloud provider
   String gcr_docker_prefix = "us.gcr.io/broad-gotc-prod/"
diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
index f324ff841c..42b92421f5 100644
--- a/pipelines/skylab/multiome/Multiome.changelog.md
+++ b/pipelines/skylab/multiome/Multiome.changelog.md
@@ -1,7 +1,8 @@
 # 5.9.5
-2024-12-12 (Date of Last Commit)
+2025-01-13 (Date of Last Commit)
 
 * Added a boolean variable is_slidetags; default is false but it is set to true if the Slide-Tags pipeline is calling Optimus
+* Added reference_gtf_file to the output h5ad unstructured metadata
 
 # 5.9.4
 2024-12-05 (Date of Last Commit)
diff --git a/pipelines/skylab/optimus/Optimus.changelog.md b/pipelines/skylab/optimus/Optimus.changelog.md
index 59f45b5005..a1df2a0575 100644
--- a/pipelines/skylab/optimus/Optimus.changelog.md
+++ b/pipelines/skylab/optimus/Optimus.changelog.md
@@ -1,8 +1,10 @@
 # 7.9.1
-2024-12-12 (Date of Last Commit)
+2025-01-13 (Date of Last Commit)
 
 * Added a boolean variable is_slidetags; set to false by default, but set to true if the Slide-Tags pipeline is calling Optimus
 
+* Added reference_gtf_file to the output h5ad unstructured metadata
+
 # 7.9.0
 2024-12-05 (Date of Last Commit)
 
diff --git a/pipelines/skylab/paired_tag/PairedTag.changelog.md b/pipelines/skylab/paired_tag/PairedTag.changelog.md
index ac48970ae8..1b272008cd 100644
--- a/pipelines/skylab/paired_tag/PairedTag.changelog.md
+++ b/pipelines/skylab/paired_tag/PairedTag.changelog.md
@@ -1,7 +1,8 @@
 # 1.9.1
-2024-12-12 (Date of Last Commit)
+2025-01-13 (Date of Last Commit)
 
-* Added a boolean variable is_slidetags. Set to true if Slide-Tags pipeline calling Optimus, otherwise false. 
+* Added a boolean variable is_slidetags; default is false, but set to true if Slide-Tags pipeline is calling Optimus
+* Added reference_gtf_file to the output h5ad unstructured metadata 
 
 # 1.9.0
 2024-12-05 (Date of Last Commit)
diff --git a/pipelines/skylab/slideseq/SlideSeq.changelog.md b/pipelines/skylab/slideseq/SlideSeq.changelog.md
index 1aecacb54c..cc1ba27ed1 100644
--- a/pipelines/skylab/slideseq/SlideSeq.changelog.md
+++ b/pipelines/skylab/slideseq/SlideSeq.changelog.md
@@ -1,7 +1,8 @@
 # 3.4.8
-2024-12-12 (Date of Last Commit)
+2025-01-13 (Date of Last Commit)
 
 *  Added a boolean variable is_slidetags; this does not affect the outputs of the pipeline
+* Added reference_gtf_file to the output h5ad unstructured metadata
 
 # 3.4.7
 2024-12-3 (Date of Last Commit)
diff --git a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
index 908720365d..2bfa234f11 100644
--- a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
+++ b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
@@ -1,7 +1,8 @@
 # 2.0.7
-2024-12-12 (Date of Last Commit)
+2025-01-13 (Date of Last Commit)
 
 *  Added a boolean variable is_slidetags; this does not affect the outputs of the pipeline
+* Added reference_gtf_file to the output h5ad unstructured metadata
 
 # 2.0.6
 2024-11-15 (Date of Last Commit)

From 343595ed15665dcc6fc48fa37ed4c153de54bcf1 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Mon, 13 Jan 2025 20:11:22 +0000
Subject: [PATCH 16/17] Updated pipeline_versions.txt with all pipeline version
 information

---
 pipeline_versions.txt | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/pipeline_versions.txt b/pipeline_versions.txt
index eb77d3561a..0c8b90a4f5 100644
--- a/pipeline_versions.txt
+++ b/pipeline_versions.txt
@@ -27,14 +27,14 @@ BroadInternalImputation	 1.1.14	2024-11-04
 BroadInternalArrays	 1.1.14	2024-11-04 
 BroadInternalRNAWithUMIs	 1.0.36	2024-11-04 
 RNAWithUMIsPipeline	 1.0.18	2024-11-04 
-Multiome	 5.9.5	2024-12-12 
-MultiSampleSmartSeq2SingleNucleus	 2.0.7	2024-12-12 
+Multiome	 5.9.5	2025-01-13 
+MultiSampleSmartSeq2SingleNucleus	 2.0.7	2025-01-13 
 BuildIndices	 3.1.0	2024-11-26 
-SlideSeq	 3.4.8	2024-12-12 
-PairedTag	 1.9.1	2024-12-12 
-atac	 2.5.3	2024-11-22 
+SlideSeq	 3.4.8	2025-01-13 
+PairedTag	 1.9.1	2025-01-13 
+atac	 2.5.4	2025-01-13 
 scATAC	 1.3.2	2023-08-03 
 snm3C	 4.0.4	2024-08-06 
-Optimus	 7.9.1	2024-12-12 
+Optimus	 7.9.1	2025-01-13 
 MultiSampleSmartSeq2	 2.2.22	2024-09-11 
 SmartSeq2SingleSample	 5.1.21	2024-09-11 

From a01cc5760e4dc32263fd0e35f59bd563f615bf7e Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Wed, 15 Jan 2025 10:32:19 -0500
Subject: [PATCH 17/17] removing unnecessary code from atac createfragmentfile

---
 pipelines/skylab/atac/atac.wdl | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl
index ddfc7c43a1..32a06b6951 100644
--- a/pipelines/skylab/atac/atac.wdl
+++ b/pipelines/skylab/atac/atac.wdl
@@ -604,16 +604,8 @@ task CreateFragmentFile {
     atac_data.uns['NHashID'] = atac_nhash_id
 
     # Add GTF to uns field
-    
     # Original path from args.annotation_file
-    gtf_path = "~{gtf_path}"  # e.g., '/cromwell_root/gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
-
-    # # Transform the path
-    # if annotation_gtf.startswith('/cromwell_root/'):
-    #     stripped_path = annotation_gtf[len('/cromwell_root/'):]  # Remove '/cromwell_root/'
-    #     updated_path = f'gs://{stripped_path}'  # Add 'gs://' prefix
-    # else:
-    #     updated_path = str(atac_gtf)
+    gtf_path = "~{gtf_path}"  # e.g., 'gs://gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
     
     atac_data.uns["reference_gtf_file"] = gtf_path
     # calculate tsse metrics