adjust configs due to nextflow bug

replikation · Jun 20, 2022 · 10656c0 · 10656c0
1 parent 304938c
commit 10656c0
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -114,6 +114,7 @@ profiles {
     }
 
     slurm {
+        includeConfig 'configs/nodes.config'
         executor {
             name = "slurm"
             queueSize = 100
@@ -122,7 +123,7 @@ profiles {
             // pollInterval = '30 sec'
         }        
         process.cache = "lenient"
-        includeConfig 'configs/nodes.config'
+
 
         process.errorStrategy = 'ignore'
     }
@@ -162,7 +163,6 @@ profiles {
     ukj_cloud { 
         workDir = "/tmp/nextflow-poreCov-$USER"
         docker { enabled = true }
-        process.executor = 'google-lifesciences'
         params.databases = 'gs://persistant-storage/poreCov/'
         bucketDir = 'gs://case-tmp-dir/poreCov/'
         google {  
@@ -177,5 +177,6 @@ profiles {
         // cloud error strategy
         process.errorStrategy = { task.exitStatus in [10,14,143,137,104,134,139] ? 'retry' : 'ignore' }
         process.maxRetries = 3
+        process.executor = 'google-lifesciences'
         }
 }