Added support for the --only-job-state option for squeue

Signed-off-by: tcutts <tim.cutts@astrazeneca.com>

Author: tcutts

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

@@ -40,6 +40,7 @@ class SlurmExecutor extends AbstractGridExecutor implements TaskArrayExecutor {
     static private Pattern SUBMIT_REGEX = ~/Submitted batch job (\d+)/
 
     private boolean perCpuMemAllocation
+    private boolean onlyJobState
 
     private boolean hasSignalOpt(TaskConfig config) {
         final opts = config.getClusterOptionsAsString()
@@ -157,7 +158,13 @@ class SlurmExecutor extends AbstractGridExecutor implements TaskArrayExecutor {
     @Override
     protected List<String> queueStatusCommand(Object queue) {
 
-        final result = ['squeue','--noheader','-o','%i %t', '-t', 'all']
+        final result = ['squeue','--noheader', '-o','%i %t', '-t', 'all']
+
+        if (onlyJobState) {
+            result << '--only-job-state'
+            // -p and -u cannot be used with --only-job-state
+            return result
+        }
 
         if( queue )
             result << '-p' << queue.toString()
@@ -213,6 +220,7 @@ class SlurmExecutor extends AbstractGridExecutor implements TaskArrayExecutor {
     void register() {
         super.register()
         perCpuMemAllocation = config.getExecConfigProp(name, 'perCpuMemAllocation', false)
+        onlyJobState = config.getExecConfigProp(name, 'onlyJobState', false)
     }
 
     @Override

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

@@ -312,6 +312,54 @@ class SlurmExecutorTest extends Specification {
         exec.queueStatusCommand('xxx') == ['squeue','--noheader','-o','%i %t','-t','all','-p','xxx','-u', usr]
     }
 
+    def 'should use onlyJobState option and omit queue and user' () {
+        given:
+        def exec = createExecutor()
+        exec.@onlyJobState = true
+
+        when:
+        def result = exec.queueStatusCommand(null)
+
+        then:
+        result == ['squeue','--noheader','-o','%i %t','-t','all','--only-job-state']
+        !result.contains('-u')
+        !result.contains('-p')
+    }
+
+    def 'should use onlyJobState option and ignore queue parameter' () {
+        given:
+        def exec = createExecutor()
+        exec.@onlyJobState = true
+
+        when:
+        def result = exec.queueStatusCommand('myqueue')
+
+        then:
+        result == ['squeue','--noheader','-o','%i %t','-t','all','--only-job-state']
+        !result.contains('-p')
+        !result.contains('myqueue')
+        !result.contains('-u')
+    }
+
+    def 'should include queue and user when onlyJobState is disabled' () {
+        given:
+        def exec = createExecutor()
+        exec.@onlyJobState = false
+
+        when:
+        def usr = System.getProperty('user.name')
+        def resultNoQueue = exec.queueStatusCommand(null)
+        def resultWithQueue = exec.queueStatusCommand('myqueue')
+
+        then:
+        resultNoQueue == ['squeue','--noheader','-o','%i %t','-t','all','-u', usr]
+        !resultNoQueue.contains('--only-job-state')
+        
+        and:
+        resultWithQueue == ['squeue','--noheader','-o','%i %t','-t','all','-p','myqueue','-u', usr]
+        !resultWithQueue.contains('--only-job-state')
+    }
+
     def 'should get array index name and start' () {
         given:
         def executor = createExecutor()