Merge pull request #7 from multimeric/error-config

Default retry error strategy
WEHI-ResearchComputing · Aug 23, 2024 · 13ecd86 · 13ecd86
2 parents 3dbf2e9 + 41d690f
commit 13ecd86
Showing 1 changed file with 24 additions and 54 deletions.
diff --git 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 }
     }
-
-
-
-
-
 }