From 7274abde35367045432f5fea63097f84dbe74982 Mon Sep 17 00:00:00 2001
From: not populated not populated <ameynert@sdf-cs1.eidf.epcc.ed.ac.uk>
Date: Mon, 22 Nov 2021 09:59:18 +0000
Subject: [PATCH] Fixed SLURM to SBATCH, short project id generation
---
submit_trio_wes_project_checksums.sh | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/submit_trio_wes_project_checksums.sh b/submit_trio_wes_project_checksums.sh
index 155a0a1..e108b2f 100755
--- a/submit_trio_wes_project_checksums.sh
+++ b/submit_trio_wes_project_checksums.sh
@@ -1,10 +1,10 @@
#!/bin/bash
-#SLURM --cpus-per-task=1
-#SLURM --mem=2GB
-#SLURM --time=6:00:00
-#SLURM --job-name=trio_whole_exome_project_checksums
-#SLURM --output=trio_whole_exome_project_checksums.%A.out
-#SLURM --error=trio_whole_exome_project_checksums.%A.err
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=2GB
+#SBATCH --time=6:00:00
+#SBATCH --job-name=trio_whole_exome_project_checksums
+#SBATCH --output=trio_whole_exome_project_checksums.%A.out
+#SBATCH --error=trio_whole_exome_project_checksums.%A.err
# Expects environment variables to be set
# PROJECT_ID - e.g. 12345_LastnameFirstname
@@ -15,6 +15,8 @@ source $CONFIG_SH
# calculate checksums on all files for this project except the families directory
+SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
+
cd $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}
rm md5sum.txt 2> /dev/null
--
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