Merge pull request #94 from NBISweden/runfile_ignore_errors

viklund · web-flow · commit e08ab31b2912 · 2017-05-08T11:27:46.000+02:00
Runfile ignore errors
diff --git a/config/devcore.config b/config/devcore.config
@@ -3,7 +3,7 @@ process {
         "-A $params.project"
     }
 
-    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'terminate' }
+    errorStrategy = { if (task.exitStatus == 143) { 'retry' } else if ( $params.runfile ) { 'ignore' } else { 'terminate' } }
     queue = 'devcore'
     executor = 'slurm'
 
diff --git a/config/standard.config b/config/standard.config
@@ -3,7 +3,7 @@ process {
         "-A $params.project"
     }
 
-    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'terminate' }
+    errorStrategy = { if (task.exitStatus == 143) { 'retry' } else if ( $params.runfile ) { 'ignore' } else { 'terminate' } }
     queue = 'core'
     executor = 'slurm'
 
diff --git a/nextflow.config b/nextflow.config
@@ -50,6 +50,7 @@ profiles {
     local {
         includeConfig 'config/milou.config'
         process.executor = 'local'
+        process.errorStrategy = { $params.runfile != "" ? 'ignore' : 'terminate' }
     }
 }
 

Original file line number	Diff line number	Diff line change
`@@ -3,7 +3,7 @@ process {`
`3`	`3`	`"-A $params.project"`
`4`	`4`	`}`
`5`	`5`
`6`		`- errorStrategy = { task.exitStatus == 143 ? 'retry' : 'terminate' }`
	`6`	`+ errorStrategy = { if (task.exitStatus == 143) { 'retry' } else if ( $params.runfile ) { 'ignore' } else { 'terminate' } }`
`7`	`7`	`queue = 'devcore'`
`8`	`8`	`executor = 'slurm'`
`9`	`9`
Original file line number	Diff line number	Diff line change
`@@ -50,6 +50,7 @@ profiles {`
`50`	`50`	`local {`
`51`	`51`	`includeConfig 'config/milou.config'`
`52`	`52`	`process.executor = 'local'`
	`53`	`+ process.errorStrategy = { $params.runfile != "" ? 'ignore' : 'terminate' }`
`53`	`54`	`}`
`54`	`55`	`}`
`55`	`56`