Merge branch 'develop' into sps_beagle_no_trailing_zeroes

salonishah11 · web-flow · commit c0798f4ef3f3 · 2026-01-27T09:45:37.000-05:00
diff --git a/pipeline_versions.txt b/pipeline_versions.txt
@@ -8,16 +8,16 @@ IlluminaGenotypingArray	 1.12.26	2025-10-09
 Imputation	 1.1.23	2025-10-03 
 ImputationBeagle	 2.5.0	2026-01-27 
 JointGenotyping	 1.7.3	2025-08-11 
-MultiSampleSmartSeq2SingleNucleus	 2.2.2	 2025-06-20 
-Multiome	 6.1.3	2025-08-15 
-Optimus	 8.0.4	25-07-31 
-PairedTag	 2.1.9	2025-09-19 
+MultiSampleSmartSeq2SingleNucleus	 2.2.3	2026-01-22 
+Multiome	 6.1.4	2026-01-22 
+Optimus	 8.0.5	2026-01-22 
+PairedTag	 2.1.10	2026-01-22 
 PeakCalling	 1.0.1	2025-08-11 
 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	 1.0.5	2025-10-24 
+SlideSeq	 3.6.4	2026-01-22 
+SlideTags	 1.0.6	2026-01-22 
 UltimaGenomicsJointGenotyping	 1.2.3	2025-08-11 
 UltimaGenomicsWholeGenomeCramOnly	 1.1.2	2025-10-09 
 UltimaGenomicsWholeGenomeGermline	 1.2.1	2025-10-09 
diff --git a/pipelines/wdl/multiome/Multiome.changelog.md b/pipelines/wdl/multiome/Multiome.changelog.md
@@ -1,3 +1,9 @@
+# 6.1.4
+2026-01-22 (Date of Last Commit)
+
+* Added a new, defaulted input cellbender_memory_GB to Optimus; this does not affect the outputs of this pipeline
+* Added a task level input, mem_size, to StarSoloFastq to expose memory settings; this does not affect the outputs of this pipeline
+
 # 6.1.3
 2025-08-15 (Date of Last Commit)
 
diff --git a/pipelines/wdl/multiome/Multiome.wdl b/pipelines/wdl/multiome/Multiome.wdl
@@ -10,7 +10,7 @@ import "../../../tasks/wdl/Utilities.wdl" as utils
 workflow Multiome {
 
 
-    String pipeline_version = "6.1.3"
+    String pipeline_version = "6.1.4"
 
 
     input {
diff --git a/pipelines/wdl/optimus/Optimus.changelog.md b/pipelines/wdl/optimus/Optimus.changelog.md
@@ -1,3 +1,9 @@
+# 8.0.5
+2026-01-22 (Date of Last Commit)
+
+* Added a new, defaulted input cellbender_memory_GB to Optimus; this does not affect the outputs of the pipeline
+* Added a task level input, mem_size, to StarSoloFastq to expose memory settings; this does not affect the outputs of this pipeline 
+
 # 8.0.4
 25-07-31 (Date of Last Commit)
 
diff --git a/pipelines/wdl/optimus/Optimus.wdl b/pipelines/wdl/optimus/Optimus.wdl
@@ -42,6 +42,7 @@ workflow Optimus {
 
     # CellBender
     Boolean run_cellbender = false
+    Int cellbender_memory_GB = 32
 
     # Chemistry options include: 2 or 3
     Int tenx_chemistry_version
@@ -73,12 +74,11 @@ workflow Optimus {
     # this pipeline does not set any preemptible varibles and only relies on the task-level preemptible settings
     # you could override the tasklevel preemptible settings by passing it as one of the workflows inputs
     # for example: `"Optimus.StarAlign.preemptible": 3` will let the StarAlign task, which by default disables the
-    # usage of preemptible machines, attempt to request for preemptible instance up to 3 times. 
-
+    # usage of preemptible machines, attempt to request for preemptible instance up to 3 times.
   }
 
   # Version of this pipeline
-  String pipeline_version = "8.0.4"
+  String pipeline_version = "8.0.5"
 
   # this is used to scatter matched [r1_fastq, r2_fastq, i1_fastq] arrays
   Array[Int] indices = range(length(r1_fastq))
@@ -233,6 +233,7 @@ workflow Optimus {
         warp_tools_docker_path = docker_prefix + warp_tools_docker
     }
   }
+
   if (count_exons  && counting_mode=="sn_rna") {
     call H5adUtils.SingleNucleusOptimusH5adOutput as OptimusH5adGenerationWithExons{
       input:
@@ -270,7 +271,7 @@ workflow Optimus {
           hardware_cpu_count = 4,
           hardware_disk_size_GB = 50,
           hardware_gpu_type = "nvidia-tesla-t4",
-          hardware_memory_GB = 32,
+          hardware_memory_GB = cellbender_memory_GB,
           hardware_preemptible_tries = 2,
           hardware_zones = "us-central1-a us-central1-c",
           nvidia_driver_version = "470.82.01"
@@ -285,7 +286,7 @@ workflow Optimus {
           hardware_cpu_count = 4,
           hardware_disk_size_GB = 50,
           hardware_gpu_type = "nvidia-tesla-t4",
-          hardware_memory_GB = 32,
+          hardware_memory_GB = cellbender_memory_GB,
           hardware_preemptible_tries = 2,
           hardware_zones = "us-central1-a us-central1-c",
           nvidia_driver_version = "470.82.01"
@@ -296,7 +297,6 @@ workflow Optimus {
   File final_h5ad_output = select_first([OptimusH5adGenerationWithExons.h5ad_output, OptimusH5adGeneration.h5ad_output])
   File final_library_metrics = select_first([OptimusH5adGenerationWithExons.library_metrics, OptimusH5adGeneration.library_metrics])
 
-
   output {
     # version of this pipeline
     String pipeline_version_out = pipeline_version
diff --git a/pipelines/wdl/paired_tag/PairedTag.changelog.md b/pipelines/wdl/paired_tag/PairedTag.changelog.md
@@ -1,3 +1,9 @@
+# 2.1.10
+2026-01-22 (Date of Last Commit)
+
+* Added a new, defaulted input cellbender_memory_GB to Optimus; this does not affect the outputs of this pipeline
+* Added a task level input, mem_size, to StarSoloFastq to expose memory settings; this does not affect the outputs of this pipeline
+
 # 2.1.9
 2025-09-19 (Date of Last Commit)
 
diff --git a/pipelines/wdl/paired_tag/PairedTag.wdl b/pipelines/wdl/paired_tag/PairedTag.wdl
@@ -9,7 +9,7 @@ import "../../../tasks/wdl/Utilities.wdl" as utils
 
 workflow PairedTag {
 
-    String pipeline_version = "2.1.9"
+    String pipeline_version = "2.1.10"
 
     input {
         String input_id
diff --git a/pipelines/wdl/slideseq/SlideSeq.changelog.md b/pipelines/wdl/slideseq/SlideSeq.changelog.md
@@ -1,3 +1,9 @@
+# 3.6.4
+2026-01-22 (Date of Last Commit)
+
+* Added a new, defaulted input cellbender_memory_GB to Optimus; this does not affect the outputs of this pipeline
+* Added a task level input, mem_size, to StarSoloFastq to expose memory settings; this does not affect the outputs of this pipeline
+
 # 3.6.3
 2025-06-20 (Date of Last Commit)
 * Added reference genome/GTF headers to fragment file via new string inputs; this change does not affect this pipeline
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 = "3.6.3"
+    String pipeline_version = "3.6.4"
 
     input {
         Array[File] r1_fastq
diff --git a/pipelines/wdl/slidetags/SlideTags.changelog.md b/pipelines/wdl/slidetags/SlideTags.changelog.md
@@ -1,3 +1,9 @@
+# 1.0.6
+2026-01-22 (Date of Last Commit)
+
+* Added a new, defaulted input cellbender_memory_GB to Optimus; this does not affect the outputs of this pipeline
+* Added a task level input, mem_size, to StarSoloFastq to expose memory settings; this does not affect the outputs of this pipeline
+
 # 1.0.5
 2025-10-24 (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 = "1.0.5"
+    String pipeline_version = "1.0.6"
 
     input {
 
diff --git a/pipelines/wdl/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md b/pipelines/wdl/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
@@ -1,3 +1,9 @@
+# 2.2.3
+2026-01-22 (Date of Last Commit)
+
+* Added a new, defaulted input cellbender_memory_GB to Optimus; this does not affect the outputs of this pipeline
+* Added a task level input, mem_size, to StarSoloFastq to expose memory settings; this does not affect the outputs of this pipeline
+
 # 2.2.2
  2025-06-20 (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 = "2.2.2"
+  String pipeline_version = "2.2.3"
 
   if (false) {
      String? none = "None"
diff --git a/tasks/wdl/StarAlign.wdl b/tasks/wdl/StarAlign.wdl
@@ -236,13 +236,12 @@ task STARsoloFastq {
     Int cpu = 16
     Int disk = 5000
     Int limitBAMsortRAM = 30
-    Int machine_mem_mb = 100 # not used in runtime -- need to remove 
+    Int mem_size = if ceil(size(r1_fastq, "GiB") + size(r2_fastq, "GiB")) <= 100 then 64 else 128
 
     # by default request non preemptible machine to make sure the slow star alignment step completes
     Int preemptible = 1
   }
 
-  Int mem_size = if ceil(size(r1_fastq, "GiB") + size(r2_fastq, "GiB")) <= 100 then 64 else 128
   Int outBAMsortingBinsN = (((ceil(size(r1_fastq, "GiB") + size(r2_fastq, "GiB")) + 50) / 100) * 100) + 100
 
   meta {
@@ -255,7 +254,7 @@ task STARsoloFastq {
     tar_star_reference: "star reference tarball built against the species that the bam_input is derived from"
     star_strand_mode: "STAR mode for handling stranded reads. Options are 'Forward', 'Reverse, or 'Unstranded'"
     samtools_star_docker_path: "(optional) the docker image containing the runtime environment for this task"
-    machine_mem_mb: "(optional) the amount of memory (MiB) to provision for this task"
+    mem_size: "the amount of memory (MiB) to provision for this task"
     cpu: "(optional) the number of cpus to provision for this task"
     disk: "(optional) the amount of disk space (GiB) to provision for this task"
     limitBAMsortRAM: "(optional) Specifies the maximum amount of RAM (in GiB) allocated for sorting BAM files in STAR. Default is 30."
