Merge pull request #270 from uclahs-cds/sfitz-strelka-retry

Sfitz strelka retry
uclahs-cds · Jan 29, 2024 · 3a7960d · 3a7960d
2 parents 1360225 + 6560630
commit 3a7960d
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Showing 6 changed files with 11 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [8.0.0-rc.1] - 2023-12-13
 
 ### Changed
+- `Strelka2` retry triggered by error code `1`
 - Use external `indexFile` function
 - Update submodules
 - Sample names sanitized for all output

diff --git a/config/F16.config b/config/F16.config
@@ -52,7 +52,7 @@ process {
         retry_strategy {
             memory {
                 strategy = 'add'
-                operand = 4.GB
+                operand = 12.GB
             }
         }
     }

diff --git a/config/F32.config b/config/F32.config
@@ -52,7 +52,7 @@ process {
         retry_strategy {
             memory {
                 strategy = 'add'
-                operand = 5.GB
+                operand = 12.GB
             }
         }
     }

diff --git a/config/F72.config b/config/F72.config
@@ -52,7 +52,7 @@ process {
         retry_strategy {
             memory {
                 strategy = 'add'
-                operand = 5.GB
+                operand = 12.GB
             }
         }
     }

diff --git a/config/base.config b/config/base.config
@@ -1,7 +1,12 @@
 process {
     cpus = { methods.check_limits( 1 * task.attempt, 'cpus' ) }
 
-    errorStrategy = { task.exitStatus in [143, 137, 104, 134, 139] ? 'retry' : 'finish' }
+    commonRetryCodes = [104, 134, 137, 139, 143, 247] // Common out-of-memory error codes
+    withName: 'call_sSNV_Strelka2' {
+        ext.retry_codes = [1] // call_sSNV_Strelka2 doesn't differentiate memory errors
+    }
+
+    errorStrategy = { task.exitStatus in (((task?.ext?.retry_codes) ? task.ext.retry_codes : []) + process.commonRetryCodes) ? 'retry' : 'terminate' }
     maxRetries = 1
 
     withLabel:process_low {

diff --git a/test/config/a_mini-strelka2.config b/test/config/a_mini-strelka2.config
@@ -17,7 +17,7 @@ params {
     dataset_id = 'TWGSAMIN'
     // set params.exome to TRUE will add the '--exome' option when running manta and strelka2
     // set params.exome to TRUE will add the '-E' option when running MuSE
-    exome = true
+    exome = false
     save_intermediate_files = true
 
     // module options