fix/update

aawdeh · aawdeh · commit d5948f98b042 · 2025-02-25T15:28:25.000-05:00
diff --git a/beta-pipelines/skylab/slidetags/SlideTags.changelog.md b/beta-pipelines/skylab/slidetags/SlideTags.changelog.md
@@ -1,5 +1,6 @@
-# 2.0.0
-2025-02-21 (Date of Last Commit)
+# 1.1.0
+2025-02-25 (Date of Last Commit)
 
 * Removed boolean variable is_slidetags; no longer needed with new updates
-* Updated the code to eliminate sharding — now, only a single instance of alignment (Starsolo) in Optimus is running. Removed tasks related to sharding and merging BAM files
+* Refactored the STAR alignment step (STARsoloFastq) in Optimus and removed tasks FastqProcessing and MergeSortBamFiles; we are no longer sharding. We are now running one instance of STAR
+
diff --git a/beta-pipelines/skylab/slidetags/SlideTags.wdl b/beta-pipelines/skylab/slidetags/SlideTags.wdl
@@ -6,7 +6,7 @@ import "../../../pipelines/skylab/optimus/Optimus.wdl" as optimus
 
 workflow SlideTags {
 
-    String pipeline_version = "2.0.0"
+    String pipeline_version = "1.1.0"
 
     input {
         # slide-tags inputs
diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
@@ -1,6 +1,6 @@
-# 6.0.0
-2025-02-21 (Date of Last Commit)
-* 
+# 5.12.0
+2025-02-25 (Date of Last Commit)
+* Refactored the STAR alignment step (STARsoloFastq) in Optimus and removed tasks FastqProcessing and MergeSortBamFiles; we are no longer sharding. We are now running one instance of STAR
 
 # 5.11.0
 2025-02-05 (Date of Last Commit)
diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
@@ -8,7 +8,7 @@ import "../../../tasks/broad/Utilities.wdl" as utils
 
 workflow Multiome {
 
-    String pipeline_version = "6.0.0"
+    String pipeline_version = "5.12.0"
 
     input {
         String cloud_provider
diff --git a/pipelines/skylab/optimus/Optimus.changelog.md b/pipelines/skylab/optimus/Optimus.changelog.md
@@ -1,9 +1,9 @@
-# 8.0.0
-2025-02-21 (Date of Last Commit)
+# 7.10.0
+2025-02-25 (Date of Last Commit)
 
 * Removed boolean variable is_slidetags; no longer needed with new updates
-* Updated the code to eliminate sharding — now, only a single instance of alignment (Starsolo) is running. Removed tasks related to sharding and merging BAM files
-* Added parameters for STARsoloFastq task, including cpu_platform_star, mem_size_star, cpu_star, disk_star, limitBAMsortRAM_star, and outBAMsortingBinsN_star
+* Refactored the STAR alignment step and removed tasks FastqProcessing and MergeSortBamFiles; we are no longer sharding. We are now running one instance of STAR
+* Added parameters for STARsoloFastq task, including cpu_platform_star, mem_size_star, cpu_star, disk_star, limitBAMsortRAM_star, and outBAMsortingBinsN_star, for dynamic allocation of resources depending on input size
 
 # 7.9.2
 2025-02-12 (Date of Last Commit)
diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
@@ -79,7 +79,7 @@ workflow Optimus {
   }
 
   # version of this pipeline
-  String pipeline_version = "8.0.0"
+  String pipeline_version = "7.10.0"
 
   # this is used to scatter matched [r1_fastq, r2_fastq, i1_fastq] arrays
   Array[Int] indices = range(length(r1_fastq))
diff --git a/pipelines/skylab/paired_tag/PairedTag.changelog.md b/pipelines/skylab/paired_tag/PairedTag.changelog.md
@@ -1,6 +1,6 @@
-# 2.0.0
-2025-02-21 (Date of Last Commit)
-* 
+# 1.11.0
+2025-02-25 (Date of Last Commit)
+* Refactored the STAR alignment step in Optimus and removed tasks FastqProcessing and MergeSortBamFiles; we are no longer sharding. We are now running one instance of STAR
 
 # 1.10.2 
 2025-02-06 (Date of Last Commit)
diff --git a/pipelines/skylab/paired_tag/PairedTag.wdl b/pipelines/skylab/paired_tag/PairedTag.wdl
@@ -8,7 +8,7 @@ import "../../../tasks/broad/Utilities.wdl" as utils
 
 workflow PairedTag {
 
-    String pipeline_version = "2.0.0"
+    String pipeline_version = "1.11.0"
 
     input {
         String input_id
diff --git a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
@@ -1,7 +1,7 @@
-# 3.0.0
-2025-02-21 (Date of Last Commit)
+# 2.1.0
+2025-02-25 (Date of Last Commit)
 
-* 
+* Refactored the STAR alignment step (STARsoloFastq) in Optimus and removed tasks FastqProcessing and MergeSortBamFiles; we are no longer sharding. We are now running one instance of STAR
 
 # 2.0.8
 2025-02-12 (Date of Last Commit)
diff --git a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl
@@ -57,7 +57,7 @@ workflow MultiSampleSmartSeq2SingleNucleus {
   }
 
   # Version of this pipeline
-  String pipeline_version = "3.0.0"
+  String pipeline_version = "2.1.0"
 
   if (false) {
      String? none = "None"
diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl
@@ -230,17 +230,18 @@ task STARsoloFastq {
     String samtools_star_docker_path
     String cpu_platform = "Intel Ice Lake"
     Int input_size = ceil(size(r1_fastq, "GiB") + size(r2_fastq, "GiB"))
-    Int mem_size = if input_size <= 100 then 64 else 128
     Int cpu = 16
     Int disk = 5000
     Int limitBAMsortRAM = 30
-    Int outBAMsortingBinsN = (input_size + 50) / 100 * 100 + 100
     Int machine_mem_mb = 100 # not used in runtime -- need to remove 
 
     # 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 {
     description: "Aligns reads in bam_input to the reference genome in tar_star_reference" 
   }

Original file line number	Diff line number	Diff line change
`@@ -79,7 +79,7 @@ workflow Optimus {`
`79`	`79`	`}`
`80`	`80`
`81`	`81`	`# version of this pipeline`
`82`		`- String pipeline_version = "8.0.0"`
	`82`	`+ String pipeline_version = "7.10.0"`
`83`	`83`
`84`	`84`	`# this is used to scatter matched [r1_fastq, r2_fastq, i1_fastq] arrays`
`85`	`85`	`Array[Int] indices = range(length(r1_fastq))`
Original file line number	Diff line number	Diff line change
`@@ -57,7 +57,7 @@ workflow MultiSampleSmartSeq2SingleNucleus {`
`57`	`57`	`}`
`58`	`58`
`59`	`59`	`# Version of this pipeline`
`60`		`- String pipeline_version = "3.0.0"`
	`60`	`+ String pipeline_version = "2.1.0"`
`61`	`61`
`62`	`62`	`if (false) {`
`63`	`63`	`String? none = "None"`