Fixed filename/folder paths at end to match new organizational structure

submit_bcbio_trio_wes.sh

@@ -34,19 +34,19 @@ cd $WORK_DIR/$FAMILY_ID
 
 bcbio_nextgen.py $CONFIG_FILE -n $SLURM_CPUS_PER_TASK -t local
 
-exit
+DATE=$(basename `tail log/bcbio-nextgen.log | grep 'Storing in local filesystem' | tail -n 1 | awk '{ print $6 }' | perl -pe "s/_${SHORT_PROJECT_ID}.+//"`)
 
-DATE=$(basename `tail log/bcbio-nextgen.log | grep 'Storing in local filesystem' | tail -n 1 | awk '{ print $6 }' | perl -pe "s/_${PROJECT_ID}.+//"`)
+FAMILY_DIR=${DATE}_${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID}
 
-if [ -e $OUTPUT_DIR/${DATE}_${SHORT_PROJECT_ID}_${FAMILY_ID} ]
+if [ -e $OUTPUT_DIR/$FAMILY_DIR ]
 then
   for INDV in `cut -f 2 $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}/params/${PROJECT_ID}_${FAMILY_ID}.ped`
   do
-    mv $OUTPUT_DIR/$INDV $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID}/
+    mv $OUTPUT_DIR/$INDV $OUTPUT_DIR/$FAMILY_DIR/
   done
 
   # fix VCF output file names
-  cd $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID}
+  cd $OUTPUT_DIR/$FAMILY_DIR
   if [ ! -e ${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz ]
   then
     PREFIX=`echo $FAMILY_ID | cut -d '_' -f 1`
@@ -55,6 +55,10 @@ then
     mv ${PREFIX}${SUFFIX}-gatk-haplotype-annotated.vcf.gz.tbi ${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz.tbi
   fi
 
+  cd $OUTPUT_DIR
+  mkdir -p ${SHORT_PROJECT_ID}_${VERSION}/families
+  mv $FAMILY_DIR ${SHORT_PROJECT_ID}_${VERSION}/families/
+
 else
   echo $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID} does not exist.
 fi