From 9e3ff60c0b1366a44f0366507913761da493d17e Mon Sep 17 00:00:00 2001
From: Mareike Janiak <mareike.janiak@computationalgenomics.ca>
Date: Wed, 10 Jun 2026 16:23:29 -0400
Subject: [PATCH] updating cit script for new chunk_and_submit_genpipes tool

---
 integration_tests.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/integration_tests.sh b/integration_tests.sh
index 367eb65..bdebb37 100755
--- a/integration_tests.sh
+++ b/integration_tests.sh
@@ -360,9 +360,8 @@ submit () {
         echo "Nothing to submit in ${command}..."
       else
         echo submitting $pipeline
-        genpipes tools chunk_genpipes ${command} ${PIPELINE_FOLDER}/chunk
         # will retry submit 10 times
-        genpipes tools submit_genpipes -l 10 -n 999 -S $SCHEDULER ${PIPELINE_FOLDER}/chunk \
+        genpipes tools chunk_and_submit_genpipes ${command} ${PIPELINE_FOLDER}/chunk -l 10 -q 999 -S $SCHEDULER \
         | tee -a ${SCRIPT_OUTPUT}/all_jobs
         RET_CODE_SUBMIT_SCRIPT=${PIPESTATUS[0]}
         ExitCodes+=(["${PIPELINE_LONG_NAME} submit"]="$RET_CODE_SUBMIT_SCRIPT")