From 41d690fd64e01c5b64bea4d024bb92c7873ff205 Mon Sep 17 00:00:00 2001
From: Michael Milton <ttmigueltt@gmail.com>
Date: Fri, 23 Aug 2024 12:12:42 +1000
Subject: [PATCH] Default retry error strategy

---
 config/modules.config | 78 +++++++++++++------------------------------
 1 file changed, 24 insertions(+), 54 deletions(-)

diff --git a/config/modules.config b/config/modules.config
index 1433fed..0c47014 100644
--- a/config/modules.config
+++ b/config/modules.config
@@ -12,86 +12,56 @@
 
 //process configurations
 process {
-    memory: '1G'
+    queue = 'regular'
+
+    // Retry any failing task up to 5 times by default
+    maxRetries = 5
+    errorStrategy = 'retry'
+
     withLabel:BWAAlign {
-        queue='regular'
         cpus = 5
-        memory={ 4.GB * task.attempt }
-        time='12h'
-        errorStrategy ={ 'retry'  }
-        maxRetries= 5
+        memory = { 4.GB * task.attempt }
+        time = '12h'
     }
     withLabel:IndexDedup {
-        queue='regular'
         cpus = 5
-        memory={ 32.GB * task.attempt }
-        time='8h'
-        errorStrategy ={ 'retry'  }
-        maxRetries= 5
+        memory = { 32.GB * task.attempt }
+        time = '8h'
     }
     withLabel:Write {
-        queue='regular'
         cpus = 1
-        memory={ 1.GB * task.attempt }
-        time='12h'
-        //errorStrategy ={ 'retry'  }
-        maxRetries= 5
+        memory = { 1.GB * task.attempt }
+        time = '12h'
+        errorStrategy = 'terminate'
     }
     withLabel:Samtools {
-        queue='regular'
         cpus = 1
-        memory={ 8.GB * task.attempt }
-        errorStrategy ={ 'retry'  }
-        maxRetries= 5
+        memory = { 8.GB * task.attempt }
     }
     withLabel:Bcftools {
-        queue='regular'
         cpus = 5
-        memory={ 8.GB * task.attempt }
-        time='12h'
-
-        //errorStrategy ={ 'retry'  }
-        maxRetries= 5
+        memory = { 8.GB * task.attempt }
+        time = '12h'
+        errorStrategy = 'terminate'
     }
     withLabel: Fastqc {
-        queue='regular'
         cpus = 5
-        memory={ 4.GB * task.attempt }
-        time='12h'
-
-        errorStrategy ={ 'retry'  }
-        maxRetries= 5
+        memory = { 4.GB * task.attempt }
+        time = '12h'
     }
     withLabel: Multiqc {
-        queue='regular'
         cpus = 2
-        memory={ 1.GB * task.attempt }
+        memory = { 1.GB * task.attempt }
         time='12h'
-
-        errorStrategy ={ 'retry'  }
-        maxRetries= 5
     }
     withLabel: Gridss {
-        queue='regular'
         cpus = 8
-        time='12h'
-        memory={ 20.GB * task.attempt }
-
-        errorStrategy ={ 'retry'  }
-        maxRetries= 5
+        time = '12h'
+        memory = { 20.GB * task.attempt }
     }
     withLabel: Rfilter {
-        queue='regular'
         cpus = 8
-        time='12h'
-        memory={ 10.GB * task.attempt }
-
-        errorStrategy ={ 'retry'  }
-        maxRetries= 5
+        time = '12h'
+        memory = { 10.GB * task.attempt }
     }
-    
-    
-   
-    
-    
 }