Merge branch 'develop' into km-buildindices-docs

broadinstitute · Dec 20, 2023 · cb32c0c · cb32c0c
2 parents 0f70c90 + 79fe930
commit cb32c0c
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Showing 5 changed files with 17 additions and 8 deletions.
diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
@@ -1,3 +1,7 @@
+# 3.0.2
+2023-12-20 (Date of Last Commit)
+* JoinMultiomeBarcodes now has dynamic memory and disk allocation
+
 # 3.0.1
 2023-12-12 (Date of Last Commit)
 * ValidateVcfs now has optional memory parameter; this does not affect this pipeline

diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
@@ -6,7 +6,7 @@ import "../../../tasks/skylab/H5adUtils.wdl" as H5adUtils
 import "https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.0/wdl/cellbender_remove_background.wdl" as CellBender
 
 workflow Multiome {
-    String pipeline_version = "3.0.1"
+    String pipeline_version = "3.0.2"
 
     input {
         String input_id

diff --git a/pipelines/skylab/optimus/Optimus.changelog.md b/pipelines/skylab/optimus/Optimus.changelog.md
@@ -1,3 +1,8 @@
+# 6.3.1
+2023-12-20 (Date of Last Commit)
+
+* JoinMultiomeBarcodes now has dynamic memory and disk allocation; this does affect the Optimus workflow
+
 # 6.3.0
 2023-12-04 (Date of Last Commit)
 

diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
@@ -64,7 +64,7 @@ workflow Optimus {
 
   # version of this pipeline
 
-  String pipeline_version = "6.3.0"
+  String pipeline_version = "6.3.1"
 
   # this is used to scatter matched [r1_fastq, r2_fastq, i1_fastq] arrays
   Array[Int] indices = range(length(r1_fastq))

diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl
@@ -192,22 +192,22 @@ task JoinMultiomeBarcodes {
     File gex_h5ad
     File gex_whitelist
     File atac_whitelist
-    Int disk_size = 500
-    Int mem_size = 16
     Int nthreads = 1
     String cpuPlatform = "Intel Cascade Lake"
   }
     String gex_base_name = basename(gex_h5ad, ".h5ad")
     String atac_base_name = basename(atac_h5ad, ".h5ad")
     String atac_fragment_base = basename(atac_fragment, ".tsv")
+
+    Int machine_mem_mb = ceil((size(atac_h5ad, "MiB") + size(gex_h5ad, "MiB") + size(atac_fragment, "MiB")) * 3) + 10000
+    Int disk =  ceil((size(atac_h5ad, "GiB") + size(gex_h5ad, "GiB") + size(atac_fragment, "GiB")) * 5) + 10
+
   parameter_meta {
     atac_h5ad: "The resulting h5ad from the ATAC workflow."
     atac_fragment: "The resulting fragment TSV from the ATAC workflow."
     gex_h5ad: "The resulting h5ad from the Optimus workflow."
     gex_whitelist: "Whitelist used for gene expression barcodes."
     atac_whitelist: "Whitelist used for ATAC barcodes."
-    disk_size: "Disk size used in create fragment file step."
-    mem_size: "The size of memory used in create fragment file."
   }
 
   command <<<
@@ -280,8 +280,8 @@ task JoinMultiomeBarcodes {
 
   runtime {
     docker: "us.gcr.io/broad-gotc-prod/snapatac2:1.0.4-2.3.1-1700590229"
-    disks: "local-disk ${disk_size} SSD"
-    memory: "${mem_size} GiB"
+    disks: "local-disk ~{disk} HDD"
+    memory: "${machine_mem_mb} MiB"
     cpu: nthreads
   }