updated Metrics dockers to latest warp-tools (broadinstitute#1130)

* updated Metrics dockers to latest warp-tools
knathamuni · Nov 20, 2023 · 4169831 · 4169831
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commit 4169831
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Showing 7 changed files with 22 additions and 7 deletions.
diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
@@ -1,3 +1,8 @@
+# 2.3.1
+2023-11-20 (Date of Last Commit)
+
+* Added the latest warp-tools docker to the Metrics task; this allows use of REFSEQ references
+
 # 2.3.0
 2023-11-03 (Date of Last Commit)
 

diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
@@ -4,7 +4,7 @@ import "../../../pipelines/skylab/multiome/atac.wdl" as atac
 import "../../../pipelines/skylab/optimus/Optimus.wdl" as optimus
 import "../../../tasks/skylab/H5adUtils.wdl" as H5adUtils
 workflow Multiome {
-    String pipeline_version = "2.3.0"
+    String pipeline_version = "2.3.1"
 
     input {
         String input_id

diff --git a/pipelines/skylab/optimus/Optimus.changelog.md b/pipelines/skylab/optimus/Optimus.changelog.md
@@ -1,4 +1,9 @@
 
+# 6.2.1
+2023-11-20 (Date of Last Commit)
+
+* Added the latest warp-tools docker to the Metrics task; this allows use of REFSEQ references
+
 # 6.2.0
 2023-11-03 (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 = "6.2.0"
+  String pipeline_version = "6.2.1"
 
   # 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/slideseq/SlideSeq.changelog.md b/pipelines/skylab/slideseq/SlideSeq.changelog.md
@@ -1,3 +1,8 @@
+# 2.1.1
+2023-11-20 (Date of Last Commit)
+
+* Added the latest warp-tools docker to the Metrics task; this allows use of REFSEQ references
+
 # 2.1.0
 2023-11-03 (Date of Last Commit)
 

diff --git a/pipelines/skylab/slideseq/SlideSeq.wdl b/pipelines/skylab/slideseq/SlideSeq.wdl
@@ -23,7 +23,7 @@ import "../../../tasks/skylab/MergeSortBam.wdl" as Merge
 
 workflow SlideSeq {
 
-    String pipeline_version = "2.1.0"
+    String pipeline_version = "2.1.1"
 
     input {
         Array[File] r1_fastq

diff --git a/tasks/skylab/Metrics.wdl b/tasks/skylab/Metrics.wdl
@@ -9,7 +9,7 @@ task CalculateCellMetrics {
 
     # runtime values
 
-    String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.8-1699023501"
+    String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.9-1700252065"
     Int machine_mem_mb = 8000
     Int cpu = 4
     Int disk = ceil(size(bam_input, "Gi") * 4) + ceil((size(original_gtf, "Gi") * 3)) 
@@ -85,7 +85,7 @@ task CalculateGeneMetrics {
     String input_id
     # runtime values
 
-    String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.8-1699023501"
+    String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.9-1700252065"
     Int machine_mem_mb = 8000
     Int cpu = 4
     Int disk = ceil(size(bam_input, "Gi") * 4) 
@@ -151,7 +151,7 @@ task CalculateUMIsMetrics {
     File? mt_genes
     String input_id
     # runtime values
-    String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.8-1699023501"
+    String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.9-1700252065"
     Int machine_mem_mb = 16000
     Int cpu = 8
     Int disk = ceil(size(bam_input, "Gi") * 4)
@@ -217,7 +217,7 @@ task FastqMetricsSlideSeq {
 
 
     # Runtime attributes
-    String docker =  "us.gcr.io/broad-gotc-prod/warp-tools:1.0.8-1699023501"
+    String docker =  "us.gcr.io/broad-gotc-prod/warp-tools:1.0.9-1700252065"
     Int cpu = 16
     Int machine_mb = 40000
     Int disk = ceil(size(r1_fastq, "GiB")*3)  + 50