diff --git a/prepare_bcbio_config_crf.sh b/prepare_bcbio_config_crf.sh
index f9e3c007b4b0d98efe88a4a3ca87078de625fdb1..65caf4201ebafc0b1415bad481c50c59db8c86f2 100755
--- a/prepare_bcbio_config_crf.sh
+++ b/prepare_bcbio_config_crf.sh
@@ -51,8 +51,8 @@ perl -pi -e 's/\r//' $PROJECT_ID.ped
 # create reads directory for project
 mkdir -p $READS_DIR/$PROJECT_ID
 
-# generate the family_ids list - makes strong assumption about relative paths!
-ls ../../data/$PROJECT_ID/*.gz | grep -v Undetermined | cut -d '/' -f 5 | cut -f 1,3 -d '_' | sort -u > $PROJECT_ID.family_ids.txt
+# generate the family_ids list
+ls $DOWNLOAD_DIR/$PROJECT_ID/*.gz | grep -v Undetermined | cut -d '/' -f 5 | cut -f 1,3 -d '_' | sort -u > $PROJECT_ID.family_ids.txt
 
 PLATE_ID=`cut -f 1 -d '_' $PROJECT_ID.family_ids.txt | sort -u`
 for FAMILY_ID in `cut -f 2 -d '_' $PROJECT_ID.family_ids.txt`
@@ -63,9 +63,12 @@ do
     > ${PROJECT_ID}_${PLATE_ID}_${FAMILY_ID}.ped
 done
 
+SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
+PREFIX=${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID}
+
 for FAMILY_ID in `cat ${PROJECT_ID}.family_ids.txt`
 do
-  echo "samplename,description,batch,sex,phenotype,variant_regions" > ${VERSION}_${PROJECT_ID}_${FAMILY_ID}.csv
+  echo "samplename,description,batch,sex,phenotype,variant_regions" > $PREFIX.csv
   COUNT=`wc -l ${PROJECT_ID}_${FAMILY_ID}.ped | awk '{ print $1 }'`
 
   for ((i=1; i<=$COUNT; i=i+1))
@@ -76,25 +79,29 @@ do
 
     for FILE in `ls $DOWNLOAD_DIR/$PROJECT_ID/*${SAMPLE}*.gz`
     do
-      echo "$FILE,$SAMPLE,$FAMILY_ID,$SEX,$PHENOTYPE,$TARGET" >> ${VERSION}_${PROJECT_ID}_${FAMILY_ID}.csv
+      echo "$FILE,$SAMPLE,$FAMILY_ID,$SEX,$PHENOTYPE,$TARGET" >> $PREFIX.csv
     done
 
   done
 
-  bcbio_prepare_samples.py --out $READS_DIR/$PROJECT_ID --csv ${VERSION}_${PROJECT_ID}_${FAMILY_ID}.csv
+  bcbio_prepare_samples.py --out $READS_DIR/$PROJECT_ID --csv $PREFIX.csv
 
-  mv ${VERSION}_${PROJECT_ID}_${FAMILY_ID}-merged.csv ${VERSION}_${PROJECT_ID}_${FAMILY_ID}.csv
+  mv $PREFIX-merged.csv $PREFIX.csv
 
   BARE_FAMILY_ID=`echo $FAMILY_ID | cut -d '_' -f 2`
 
-  bcbio_nextgen.py -w template $BCBIO_TEMPLATE ${VERSION}_${PROJECT_ID}_${FAMILY_ID}.csv $READS_DIR/$PROJECT_ID/*_${BARE_FAMILY_ID}_R[12].fastq.gz
+  bcbio_nextgen.py -w template $BCBIO_TEMPLATE $PREFIX.csv $READS_DIR/$PROJECT_ID/*_${BARE_FAMILY_ID}_R[12].fastq.gz
 
-  mv ${VERSION}_${PROJECT_ID}_${FAMILY_ID}/config/${VERSION}_${PROJECT_ID}_${FAMILY_ID}.yaml $CONFIG_DIR/
+  mv $PREFIX/config/$PREFIX.yaml $CONFIG_DIR/
 
   COMPRESSED_ID=`echo "$FAMILY_ID" | perl -pe "s/\_//"`
 
-  perl -i -pe "s/${COMPRESSED_ID}/${FAMILY_ID}/" $CONFIG_DIR/${VERSION}_${PROJECT_ID}_${FAMILY_ID}.yaml
+  perl -i -pe "s/${COMPRESSED_ID}/${FAMILY_ID}/" $CONFIG_DIR/$PREFIX.yaml
+
+  rm -r $PREFIX
 
-  rm -r ${VERSION}_${PROJECT_ID}_${FAMILY_ID}
+  mkdir -p ${OUTPUT_DIR}/${SHORT_PROJECT_ID}_${VERSION}/params/
+  mv ${PREFIX}.csv ${OUTPUT_DIR}/${SHORT_PROJECT_ID}_${VERSION}/params/
+  mv ${PROJECT_ID}_${FAMILY_ID}.ped ${OUTPUT_DIR}/${SHORT_PROJECT_ID}_${VERSION}/params/
 
 done