Fix submit command in error message for grid executors that pipe wrap…

…per script (#3548)


Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy

@@ -185,7 +185,7 @@ class GridTaskHandler extends TaskHandler {
             final exitStatus = process.waitFor()
 
             if( exitStatus ) {
-                throw new ProcessNonZeroExitStatusException("Failed to submit process to grid scheduler for execution", result, exitStatus, builder.command())
+                throw new ProcessNonZeroExitStatusException("Failed to submit process to grid scheduler for execution", result, exitStatus, launchCmd0(builder,pipeScript))
             }
 
             // -- return the process stdout
@@ -199,6 +199,15 @@ class GridTaskHandler extends TaskHandler {
             process.destroy()
         }
     }
+
+    protected List<String> launchCmd0(ProcessBuilder builder, String pipeScript) {
+        if( !pipeScript )
+            return builder.command()
+        final result = new ArrayList(builder.command())
+        result.add('<')
+        result.add(TaskRun.CMD_RUN)
+        return result
+    }
 
     /*
      * {@inheritDocs}

modules/nextflow/src/test/groovy/nextflow/executor/GridTaskHandlerTest.groovy

@@ -67,4 +67,17 @@ class GridTaskHandlerTest extends Specification {
         task.exitStatus == 10
 
     }
+
+    def 'should create launch command' () {
+        given:
+        def builder = new ProcessBuilder().command(CMD)
+        def exec = Spy(GridTaskHandler)
+        expect:
+        exec.launchCmd0(builder, PIPE) == EXPECTED
+
+        where:
+        CMD         | PIPE  | EXPECTED
+        ['qsub']    | null  | ['qsub']
+        ['qsub']    | 'xyz' | ['qsub', '<', '.command.run']
+    }
 }