Merge pull request nf-core#672 from nf-core/eva-picard-exitstauts

Add java related retries to picard
maxulysse · Apr 19, 2024 · b685fce · b685fce
2 parents 60479ef + 16502fd
commit b685fce
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
@@ -190,6 +190,7 @@ process {
 
     withName: picard_addorreplacereadgroups {
         clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
+        errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
     }
 
     withName: genotyping_ug {
@@ -378,6 +379,7 @@ profiles {
 
             withName: picard_addorreplacereadgroups {
                 clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
+                errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
             }
 
             withName: genotyping_ug {
@@ -559,6 +561,7 @@ profiles {
 
             withName: picard_addorreplacereadgroups {
                 clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
+                errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
             }
 
             withName: genotyping_ug {