Add array jobs to CRG executor

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
nextflow-io · Sep 15, 2023 · 28dbe47 · 28dbe47
1 parent 68ea23f
commit 28dbe47
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/CrgExecutor.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/CrgExecutor.groovy
@@ -18,6 +18,7 @@ package nextflow.executor
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+import nextflow.processor.TaskArray
 import nextflow.processor.TaskRun
 /**
  * An executor specialised for CRG cluster
@@ -41,6 +42,11 @@ class CrgExecutor extends SgeExecutor {
             task.config.penv = 'smp'
         }
 
+        if( task instanceof TaskArray ) {
+            final arraySize = task.getArraySize()
+            result << '-t' << "1-${arraySize}".toString()
+        }
+
         result << '-N' << getJobNameFor(task)
         result << '-o' << quote(task.workDir.resolve(TaskRun.CMD_LOG))
         result << '-j' << 'y'