dev to staging

pipeline_versions.txt

@@ -1,12 +1,12 @@
-ArrayImputationQC	 1.2.2	2025-10-07 
+ArrayImputationQC	 1.2.3 	2025-10-17 
 ArrayImputationQuotaConsumed	 1.1.0	2025-09-29 
 BuildIndices	 5.0.0	2025-09-30 
 CramToUnmappedBams	 1.1.3	2024-08-02 
 ExomeGermlineSingleSample	 3.2.6	2025-10-09 
 ExomeReprocessing	 3.3.6	2025-10-09 
 IlluminaGenotypingArray	 1.12.26	2025-10-09 
 Imputation	 1.1.23	2025-10-03 
-ImputationBeagle	 2.2.3	2025-10-07 
+ImputationBeagle	 2.2.4	2025-10-17 
 JointGenotyping	 1.7.3	2025-08-11 
 MultiSampleSmartSeq2SingleNucleus	 2.2.2	 2025-06-20 
 Multiome	 6.1.3	2025-08-15 
@@ -17,7 +17,7 @@ Pipeline Name	Version	Date of Last Commit
 RNAWithUMIsPipeline	 1.0.19	2025-08-11 
 ReblockGVCF	 2.4.3	2025-10-09 
 SlideSeq	 3.6.3	2025-06-20 
-SlideTags	 1.0.4	2025-10-03 
+SlideTags	 1.0.5	2025-10-24 
 UltimaGenomicsJointGenotyping	 1.2.3	2025-08-11 
 UltimaGenomicsWholeGenomeCramOnly	 1.1.2	2025-10-09 
 UltimaGenomicsWholeGenomeGermline	 1.2.1	2025-10-09 

pipelines/wdl/arrays/imputation_beagle/ImputationBeagle.changelog.md

@@ -1,3 +1,8 @@
+# 2.2.4
+2025-10-17 (Date of Last Commit)
+
+* Update input_qc_version to 1.2.3 to match latest changes in InputQC wdl
+
 # 2.2.3
 2025-10-07 (Date of Last Commit)
 

pipelines/wdl/arrays/imputation_beagle/ImputationBeagle.wdl

@@ -5,8 +5,8 @@ import "../../../../tasks/wdl/ImputationTasks.wdl" as tasks
 import "../../../../tasks/wdl/ImputationBeagleTasks.wdl" as beagleTasks
 
 workflow ImputationBeagle {
-  String pipeline_version = "2.2.3"
-  String input_qc_version = "1.2.2"
+  String pipeline_version = "2.2.4"
+  String input_qc_version = "1.2.3"
   String quota_consumed_version = "1.1.0"
 
   input {

pipelines/wdl/arrays/imputation_beagle/input_qc/ArrayImputationQC.changelog.md

@@ -1,3 +1,8 @@
+# 1.2.3 
+2025-10-17 (Date of Last Commit)
+
+* Update QcChecks task to improve error messages.
+
 # 1.2.2
 2025-10-07 (Date of Last Commit)
 
@@ -6,7 +11,7 @@
 # 1.2.1
 2025-10-01 (Date of Last Commit)
 
-* Add check for vcf being bgzipped and in sorted order
+* Add check for vcf being bgzipped and in sorted order.
 
 # 1.2.0
 2025-09-29 (Date of Last Commit)
@@ -21,12 +26,12 @@
 # 1.0.3
 2025-09-15 (Date of Last Commit)
 
-* Add instruction for updating ImputationBeagle wdl when this workflow's pipeline_version changes for improved version tracking across wdls
+* Add instruction for updating ImputationBeagle wdl when this workflow's pipeline_version changes for improved version tracking across wdls.
 
 # 1.0.2
 2025-09-03 (Date of Last Commit)
 
-* Add optional pipeline_header_line input to match beagle imputation pipeline inputs
+* Add optional pipeline_header_line input to match beagle imputation pipeline inputs.
 
 # 1.0.1
 2025-08-26 (Date of Last Commit)

pipelines/wdl/arrays/imputation_beagle/input_qc/ArrayImputationQC.wdl

@@ -4,7 +4,7 @@ import "../../../../../tasks/wdl/ImputationBeagleQcTasks.wdl" as tasks
 
 workflow InputQC {
     # if this changes, update the input_qc_version value in ImputationBeagle.wdl
-    String pipeline_version = "1.2.2"
+    String pipeline_version = "1.2.3"
 
 
     input {

pipelines/wdl/arrays/imputation_beagle/input_qc/test_inputs/Plumbing/HGDP1000G_500_qc_fails_multiple_errors.json

@@ -0,0 +1,8 @@
+{
+    "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/test_qc_v3_no_data_not_bgzipped.vcf.gz",
+    "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+    "ArrayImputationQC.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",
+    "ArrayImputationQC.contigs": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
+    "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ArrayImputationQC.output_basename": "plumbing_test_fail_multiple_errors"
+}

pipelines/wdl/slidetags/SlideTags.changelog.md

@@ -1,3 +1,8 @@
+# 1.0.5
+2025-10-24 (Date of Last Commit)
+
+* Updated the positioning.wdl code to the latest version from the Macosko Lab repository to incorporate recent improvements
+
 # 1.0.4
 2025-10-03 (Date of Last Commit)
 

pipelines/wdl/slidetags/SlideTags.wdl

@@ -6,7 +6,7 @@ import "../optimus/Optimus.wdl" as optimus
 
 workflow SlideTags {
 
-    String pipeline_version = "1.0.4"
+    String pipeline_version = "1.0.5"
 
     input {
 
@@ -19,13 +19,13 @@ workflow SlideTags {
         # Optimus inputs
         Array[File] gex_r1_fastq
         Array[File] gex_r2_fastq
-        Array[File]? gex_i1_fastq        
+        Array[File]? gex_i1_fastq
         File tar_star_reference
         File annotations_gtf
         File gex_whitelist
         String cloud_provider = "gcp"
         String input_id
-        Int expected_cells = 3000 
+        Int expected_cells = 3000
         String counting_mode = "sn_rna"
         Int tenx_chemistry_version = 3
         Int emptydrops_lower = 100
@@ -39,13 +39,13 @@ workflow SlideTags {
 
         String docker = "us.gcr.io/broad-gotc-prod/slide-tags:1.2.0"
      }
-    
+
     parameter_meta {
         spatial_fastq: "Array of paths to spatial fastq files"
         pucks: "Array of paths to puck files"
         docker: "Docker image to use"
     }
-    
+
     # Call the optimus workflow
     call optimus.Optimus as Optimus {
         input:
@@ -69,8 +69,8 @@ workflow SlideTags {
             count_exons = count_exons,
             soloMultiMappers = soloMultiMappers,
             gex_expected_cells = expected_cells
-    } 
-    
+    }
+
     call SpatialCount.count as spatial_count {
         input:
             fastq_paths = spatial_fastq,
@@ -92,13 +92,13 @@ workflow SlideTags {
         # Version of Optimus pipeline
         String optimus_pipeline_version_out = Optimus.pipeline_version_out
         File optimus_genomic_reference_version = Optimus.genomic_reference_version
-   
+
         # Optimus Metrics outputs
         File optimus_cell_metrics = Optimus.cell_metrics
         File optimus_gene_metrics = Optimus.gene_metrics
         File? optimus_cell_calls = Optimus.cell_calls
-   
-        # Optimus Star outputs 
+
+        # Optimus Star outputs
         File optimus_library_metrics = Optimus.library_metrics
         File optimus_bam = Optimus.bam
         File optimus_matrix = Optimus.matrix
@@ -111,10 +111,10 @@ workflow SlideTags {
         File? optimus_multimappers_Uniform_matrix = Optimus.multimappers_Uniform_matrix
         File? optimus_multimappers_Rescue_matrix = Optimus.multimappers_Rescue_matrix
         File? optimus_multimappers_PropUnique_matrix = Optimus.multimappers_PropUnique_matrix
-    
+
         # Optimus H5ad
         File optimus_h5ad_output_file = Optimus.h5ad_output_file
-        
+
         # Optimus Cellbender outputs
         File? cb_cell_barcodes_csv = Optimus.cell_barcodes_csv
         File? cb_checkpoint_file = Optimus.checkpoint_file
@@ -134,6 +134,7 @@ workflow SlideTags {
         File positioning_summary_pdf = positioning.summary_pdf
         File positioning_intermediates = positioning.intermediates_file
         File positioning_positioning_log = positioning.positioning_log
+
      }
 }
 

tasks/wdl/ImputationBeagleQcTasks.wdl

@@ -11,10 +11,6 @@ task QcChecks {
         Int memory_mb = 4000
         Int disk_size_gb = ceil(1.1*size(vcf_input, "GiB")) + 10
     }
-    Int command_mem = memory_mb - 1500
-    Int max_heap = memory_mb - 1000
-
-    String vcf_basename = basename(vcf_input)
 
     String ref_dict_basename = basename(ref_dict)
 
@@ -25,7 +21,7 @@ task QcChecks {
         # check for a large number of variants in input vcf and exit if greater than 10 million
         line_count=$(bcftools stats ~{vcf_input}  | grep "number of records:" | awk '{print $6}')
         if [ "$line_count" -gt 10000000 ]; then
-            echo "Greater than 10 million variants found in input VCF." >> qc_messages.txt
+            echo "Greater than 10 million variants found in the input VCF." >> qc_messages.txt
             echo "false" > passes_qc.txt
             exit 0
         else
@@ -56,19 +52,38 @@ task QcChecks {
         done
 
         if [ ${#filtered_chromosomes[@]} -eq 0 ]; then
-            echo "Input must include data for at least one chromosome in the allowed contigs (${allowed_chromosomes[*]})." >> qc_messages.txt
+            echo "No variant data found for any chromosome in the supported contigs: (${allowed_chromosomes[*]})." >> qc_messages.txt
         else
-            echo "Found data for chromosomes: ${filtered_chromosomes[*]}."
+            echo "Found variants for chromosomes: ${filtered_chromosomes[*]}."
         fi
 
         # check for sorted or non bgzf compressed vcf
         bcftools index -t ~{vcf_input} 2> index_stderr.txt
+
+        # note if both of these are true, only BGZF error will be reported because indexing stops after that error
+        NOT_SORTED_MESSAGE="Input VCF is not sorted."
         if grep -qiE "unsorted positions|not continuous" index_stderr.txt; then
-            echo "Input VCF is not sorted." >> qc_messages.txt;
+            echo "${NOT_SORTED_MESSAGE}" >> qc_messages.txt;
         fi
 
+        NOT_BGZF_MESSAGE="Input VCF is not BGZF compressed."
         if grep -q "not BGZF compressed" index_stderr.txt; then
-            echo "Input VCF is not BGZF compressed." >> qc_messages.txt;
+            echo "${NOT_BGZF_MESSAGE}" >> qc_messages.txt;
+        fi
+
+        if [ -f "~{vcf_input}.tbi" ]; then
+            echo "Input VCF indexed successfully. It therefore is sorted and bgzf-compressed."
+        else
+            # only add a message if there are not index-related errors already
+            if ! grep -q "${NOT_SORTED_MESSAGE}" qc_messages.txt && ! grep -q "${NOT_BGZF_MESSAGE}" qc_messages.txt; then
+                echo "Failed to index input VCF for an unknown reason." >> qc_messages.txt
+                # echo index stderr to logs for debugging
+                echo "Contents of index_stderr.txt:"
+                cat index_stderr.txt
+            fi
+            echo "false" > passes_qc.txt
+            # exit now if indexing failed, since ValidateVariants requires an index
+            exit 0
         fi
 
         # check reference header lines if they exist
@@ -78,9 +93,8 @@ task QcChecks {
         --validation-type-to-exclude ALL \
         2> gatk_output.txt
 
-        ref_dict_basename="~{ref_dict_basename}"
         if grep -q "incompatible contigs" gatk_output.txt; then
-            echo "Found incompatible contigs (against reference dictionary $ref_dict_basename) in VCF header." >> qc_messages.txt;
+            echo "VCF header contains none of the expected contigs." >> qc_messages.txt
         else
             echo "No incompatible contigs found in VCF header."
         fi

tasks/wdl/slidetags_utils/positioning.wdl

@@ -20,10 +20,10 @@ task generate_positioning {
     gcloud config set storage/thread_count  2 # is this set by user?
 
     # Download the scripts -- these need to be changed -- also need to add to docker
-    wget https://raw.githubusercontent.com/MacoskoLab/Macosko-Pipelines/e7a4fe892acb47e8e83c1ee585109c99c946e94a/slide-tags/run-positioning.R
-    wget https://raw.githubusercontent.com/MacoskoLab/Macosko-Pipelines/e7a4fe892acb47e8e83c1ee585109c99c946e94a/slide-tags/positioning.R
-    wget https://raw.githubusercontent.com/MacoskoLab/Macosko-Pipelines/e7a4fe892acb47e8e83c1ee585109c99c946e94a/slide-tags/helpers.R
-    wget https://raw.githubusercontent.com/MacoskoLab/Macosko-Pipelines/e7a4fe892acb47e8e83c1ee585109c99c946e94a/slide-tags/plots.R
+    wget https://raw.githubusercontent.com/MacoskoLab/Macosko-Pipelines/261750c2e15da5ff17533150b62578dda629da08/slide-tags/run-positioning.R
+    wget https://raw.githubusercontent.com/MacoskoLab/Macosko-Pipelines/261750c2e15da5ff17533150b62578dda629da08/slide-tags/positioning.R
+    wget https://raw.githubusercontent.com/MacoskoLab/Macosko-Pipelines/261750c2e15da5ff17533150b62578dda629da08/slide-tags/helpers.R
+    wget https://raw.githubusercontent.com/MacoskoLab/Macosko-Pipelines/261750c2e15da5ff17533150b62578dda629da08/slide-tags/plots.R
 
     echo "RNA: ~{sep=' ' rna_paths}"
     echo "SB: ~{sb_path}"

website/docs/Pipelines/SlideTags_Pipeline/README.md

@@ -158,17 +158,16 @@ All releases of the pipeline are documented in the repository’s changelog.
 
 ## Citing the Slide-tags Pipeline
 
-If you use the Slide-tags Pipeline in your research, please cite the original sources:
-
-- **Macosko Lab Pipelines:** https://github.com/MacoskoLab/Macosko-Pipelines/tree/main/slide-tags
+If you use the Slide-tags Pipeline in your research, please identify the pipeline in your methods section using the [Slide-tags SciCrunch resource identifier](https://scicrunch.org/resources/data/record/nlx_144509-1/SCR_027567/resolver?q=SCR_027567&l=SCR_027567&i=rrid:SCR_027567).
+* Ex: *Slide-tags Pipeline (RRID:SCR_027567)*
 
 Please also consider citing our preprint:
 
 Degatano, K., Awdeh, A., Cox III, R.S., Dingman, W., Grant, G., Khajouei, F., Kiernan, E., Konwar, K., Mathews, K.L., Palis, K., et al. Warp Analysis Research Pipelines: Cloud-optimized workflows for biological data processing and reproducible analysis. Bioinformatics 2025; btaf494. https://doi.org/10.1093/bioinformatics/btaf494
 
 ## Acknowledgements
 
-We are immensely grateful Matthew Shabet and the Macosko Lab for development of these analsyes, for their generous time making these scripts FAIR, and for the many hours working with the WARP team to incoporate the scripts into WDL. 
+We are immensely grateful to Matthew Shabet and the Macosko Lab for the development of these analyses, for their generous time in making these scripts FAIR, and for the many hours spent working with the WARP team to incorporate the scripts into WDL.
 
 ## Feedback