Fixed filename fixing

submit_bcbio_trio_wes.sh

@@ -41,10 +41,12 @@ then
 
   # 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