Merge pull request broadinstitute#477 from broadinstitute/gg_AddRetri…

…esForFingerprintingTasks Made Fingerprint pull/push tasks be retriable.
vivbak · Oct 26, 2021 · 85888db · 85888db
2 parents fba9a17 + d326df3
commit 85888db
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Showing 3 changed files with 16 additions and 6 deletions.
diff --git a/pipelines/broad/arrays/single_sample/Arrays.changelog.md b/pipelines/broad/arrays/single_sample/Arrays.changelog.md
@@ -1,3 +1,9 @@
+# 2.5.1
+2021-10-25
+
+* Make fingerprint retrieval and storage tasks use max_retries to enable recovery from transient failures
+* Modified Arrays pipeline to not read fingerprints for control samples from the Mercury Fingerprint Store.
+
 # 2.5.0
 2021-10-07
 

diff --git a/pipelines/broad/arrays/single_sample/Arrays.wdl b/pipelines/broad/arrays/single_sample/Arrays.wdl
@@ -23,7 +23,7 @@ import "../../../../tasks/broad/Utilities.wdl" as utils
 
 workflow Arrays {
 
-  String pipeline_version = "2.5.0"
+  String pipeline_version = "2.5.1"
 
   input {
     String chip_well_barcode
@@ -294,7 +294,7 @@ workflow Arrays {
 
   Int analysis_version = select_first([analysis_version_number, GetNextArraysQcAnalysisVersionNumber.analysis_version_number])
 
-  if (read_fingerprint_from_mercury) {
+  if (read_fingerprint_from_mercury && (!defined(control_sample_name))) {
     call InternalTasks.MakeSafeFilename {
       input:
         name = sample_alias

diff --git a/tasks/broad/InternalTasks.wdl b/tasks/broad/InternalTasks.wdl
@@ -44,7 +44,8 @@ task DownloadGenotypes {
     String environment
     File vault_token_path
 
-    Int preemptible_tries
+    Int? max_retries
+    Int? preemptible_tries
   }
 
   meta {
@@ -111,7 +112,8 @@ task DownloadGenotypes {
   runtime {
     docker: "us.gcr.io/broad-arrays-prod/arrays-picard-private:4.1.0-1631191359"
     memory: "3.5 GiB"
-    preemptible: preemptible_tries
+    maxRetries: select_first([max_retries, 2])
+    preemptible: select_first([preemptible_tries, 3])
   }
 
   output {
@@ -130,7 +132,8 @@ task UploadFingerprintToMercury {
     String environment
     File vault_token_path
 
-    Int preemptible_tries
+    Int? max_retries
+    Int? preemptible_tries
   }
 
   command <<<
@@ -161,6 +164,7 @@ task UploadFingerprintToMercury {
   runtime {
     docker: "us.gcr.io/broad-arrays-prod/arrays-picard-private:4.1.0-1631191359"
     memory: "3.5 GiB"
-    preemptible: preemptible_tries
+    maxRetries: select_first([max_retries, 2])
+    preemptible: select_first([preemptible_tries, 3])
   }
 }