From 2b06293f64b8f81fe4ae8799e13d38ab5bcd7f67 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 8 Feb 2022 11:15:17 +0100
Subject: [PATCH] Read add empty BAM exit code for qualitmap 255

---
 conf/pipeline/eager/eva.config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index d13a71a..d436895 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -139,7 +139,7 @@ process {
 
   withName: qualimap {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
-    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
    }
 
   withName: damageprofiler {
@@ -322,7 +322,7 @@ profiles {
 
         withName: qualimap {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
-          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
         }
 
         withName: damageprofiler {
@@ -505,7 +505,7 @@ profiles {
 
         withName: qualimap {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
-          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
         }
 
         withName: damageprofiler {