From 7abf48a48967b65ac3b1f5693af9847d13f8086d Mon Sep 17 00:00:00 2001
From: not populated not populated <ameynert@sdf-cs1.eidf.epcc.ed.ac.uk>
Date: Sat, 2 Oct 2021 08:51:12 +0100
Subject: [PATCH] Slurm scheduler can handle single index job array submission

---
 submit_bcbio_trio_wes.sh | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/submit_bcbio_trio_wes.sh b/submit_bcbio_trio_wes.sh
index 7d20d95..93654af 100755
--- a/submit_bcbio_trio_wes.sh
+++ b/submit_bcbio_trio_wes.sh
@@ -6,17 +6,6 @@
 #SBATCH --output=trio_whole_exome_bcbio.%A_%a.out
 #SBATCH --error=trio_whole_exome_bcbio.%A_%a.err
 
-# enable running singletons
-if [ -z $SLURM_ARRAY_TASK_ID ]
-then
-  if [ -z $INDEX ]
-  then
-    export SLURM_ARRAY_TASK_ID=1
-  else
-    export SLURM_ARRAY_TASK_ID=$INDEX
-  fi
-fi
-
 # Expects environment variables to be set
 # PROJECT_ID - e.g. 12345_LastnameFirstname
 # CONFIG_SH - absolute path to configuration script setting environment variables
-- 
GitLab