From ad9322c4f26045f9d80d8680043579f48509363a Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Fri, 18 Oct 2019 19:10:30 +0100
Subject: [PATCH] Fixed filename fixing
---
submit_bcbio_trio_wes.sh | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/submit_bcbio_trio_wes.sh b/submit_bcbio_trio_wes.sh
index 9fd1274..a03a424 100755
--- a/submit_bcbio_trio_wes.sh
+++ b/submit_bcbio_trio_wes.sh
@@ -41,10 +41,12 @@ then
#Â fix VCF output file names
cd $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID}
- if [ -e ${PROJECT_ID}${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz ]
+ if [ ! -e ${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
+ PREFIX=`echo $FAMILY_ID | cut -d '_' -f 1`
+ SUFFIX=`echo $FAMILY_ID | cut -d '_' -f 2`
+ mv ${PREFIX}${SUFFIX}-gatk-haplotype-annotated.vcf.gz ${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz
+ mv ${PREFIX}${SUFFIX}-gatk-haplotype-annotated.vcf.gz.tbi ${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz.tbi
fi
else
--
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