Fix job array syntax for PBS/Torque executor (#5281) [ci fast]

Signed-off-by: Ben Sherman <[email protected]>
nextflow-io · Sep 3, 2024 · d59f5fa · d59f5fa
1 parent 5a01f27
commit d59f5fa
Show file tree

Hide file tree

Showing 3 changed files with 9 additions and 4 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/PbsExecutor.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/PbsExecutor.groovy
@@ -46,7 +46,7 @@ class PbsExecutor extends AbstractGridExecutor implements TaskArrayExecutor {
 
         if( task instanceof TaskArrayRun ) {
             final arraySize = task.getArraySize()
-            result << '-J' << "0-${arraySize - 1}".toString()
+            result << '-t' << "0-${arraySize - 1}".toString()
         }
 
         result << '-N' << getJobNameFor(task)
@@ -188,7 +188,7 @@ class PbsExecutor extends AbstractGridExecutor implements TaskArrayExecutor {
 
     @Override
     String getArrayIndexName() {
-        return 'PBS_ARRAY_INDEX'
+        return 'PBS_ARRAYID'
     }
 
     @Override

diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/PbsProExecutor.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/PbsProExecutor.groovy
@@ -129,4 +129,9 @@ class PbsProExecutor extends PbsExecutor {
         DECODE_STATUS.get(status)
     }
 
+    @Override
+    String getArrayIndexName() {
+        return 'PBS_ARRAY_INDEX'
+    }
+
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/PbsExecutorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/PbsExecutorTest.groovy
@@ -172,7 +172,7 @@ class PbsExecutorTest extends Specification {
         }
         then:
         executor.getHeaders(taskArray) == '''
-                #PBS -J 0-4
+                #PBS -t 0-4
                 #PBS -N nf-task_name
                 #PBS -o /dev/null
                 #PBS -j oe
@@ -321,7 +321,7 @@ class PbsExecutorTest extends Specification {
         given:
         def executor = Spy(PbsExecutor)
         expect:
-        executor.getArrayIndexName() == 'PBS_ARRAY_INDEX'
+        executor.getArrayIndexName() == 'PBS_ARRAYID'
         executor.getArrayIndexStart() == 0
     }