From ab9dbf25bfcb8d3d01dc98c7daa21a0212b19186 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Wed, 16 Oct 2019 12:06:22 +0100
Subject: [PATCH] Added fix of VCF output file names
---
submit_bcbio_trio_wes.sh | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/submit_bcbio_trio_wes.sh b/submit_bcbio_trio_wes.sh
index 984e80d..9fd1274 100755
--- a/submit_bcbio_trio_wes.sh
+++ b/submit_bcbio_trio_wes.sh
@@ -41,8 +41,11 @@ then
#Â fix VCF output file names
cd $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID}
- mv ${PROJECT_ID}${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz ${PROJECT_ID}_${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz
- mv ${PROJECT_ID}${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz.tbi ${PROJECT_ID}_${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz.tbi
+ if [ -e ${PROJECT_ID}${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz ]
+ then
+ mv ${PROJECT_ID}${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz ${PROJECT_ID}_${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz
+ mv ${PROJECT_ID}${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz.tbi ${PROJECT_ID}_${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz.tbi
+ fi
else
echo $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID} does not exist.
--
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