From 0471dff3967a2e99e6c11bde15f6eb433822cc37 Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Thu, 21 Nov 2024 10:58:51 +0000
Subject: [PATCH] Fix PBSPRO queue status fetch

Signed-off-by: HDash <16350928+HDash@users.noreply.github.com>
---
 .../src/main/groovy/nextflow/executor/PbsProExecutor.groovy     | 2 +-
 .../src/test/groovy/nextflow/executor/PbsProExecutorTest.groovy | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/PbsProExecutor.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/PbsProExecutor.groovy
index bcb0cbfa84..4bfbf6920a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/PbsProExecutor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/PbsProExecutor.groovy
@@ -104,7 +104,7 @@ class PbsProExecutor extends PbsExecutor {
         if( queue ) {
             cmd += queue
         } else {
-            cmd += '$( qstat -B | grep -E -v \'(^Server|^---)\' | awk -v ORS=\' \' \'{print \"@\"\$1}\' )'
+            cmd += '$( qstat -B | grep -E -v \'(^Server|^---)\' | awk -v ORS=\' \' \'{if (\$1 != \"\") print \"@\"\$1}\' )'
         }
         return ['bash','-c', "set -o pipefail; $cmd | { grep -E '(Job Id:|job_state =)' || true; }".toString()]
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/PbsProExecutorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/PbsProExecutorTest.groovy
index b9b4ec164b..4de6bd3e28 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/PbsProExecutorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/PbsProExecutorTest.groovy
@@ -211,7 +211,7 @@ class PbsProExecutorTest extends Specification {
         def executor = [:] as PbsProExecutor
 
         expect:
-        executor.queueStatusCommand(null) == ['bash','-c', "set -o pipefail; qstat -f \$( qstat -B | grep -E -v '(^Server|^---)' | awk -v ORS=' ' '{print \"@\"\$1}' ) | { grep -E '(Job Id:|job_state =)' || true; }"]
+        executor.queueStatusCommand(null) == ['bash','-c', "set -o pipefail; qstat -f \$( qstat -B | grep -E -v '(^Server|^---)' | awk -v ORS=' ' '{if (\$1 != \"\") print \"@\"\$1}' ) | { grep -E '(Job Id:|job_state =)' || true; }"]
         executor.queueStatusCommand('xxx') == ['bash','-c', "set -o pipefail; qstat -f xxx | { grep -E '(Job Id:|job_state =)' || true; }"]
         executor.queueStatusCommand('xxx').each { assert it instanceof String }
     }