Changed to using short project id, version comes after project id, per-family...

Changed to using short project id, version comes after project id, per-family PED and CSV files move to results/project_version/params folder

prepare_bcbio_config.sh

@@ -54,9 +54,15 @@ cat $DOWNLOAD_DIR/$PROJECT_ID/*/file_list.tsv | \
     --ped $PROJECT_ID.ped \
     --suffix $SAMPLE_SUFFIX
 
+SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
+
+mkdir -p ${OUTPUT_DIR}/${SHORT_PROJECT_ID}_${VERSION}/params
+
 for FAMILY_ID in `cat ${PROJECT_ID}.family_ids.txt`
 do
-  echo "samplename,description,batch,sex,phenotype,variant_regions" > ${VERSION}_${PROJECT_ID}_${FAMILY_ID}.csv
+  PREFIX=${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID}
+  
+  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))
@@ -90,26 +96,28 @@ do
 
     for FILE in `ls $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/*_R[1,2].fastq.gz`
     do
-      echo "$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 ${VERSION}_${PROJECT_ID}_${FAMILY_ID}
+  rm -r ${PREFIX}
+  mv ${PREFIX}.csv ${OUTPUT_DIR}/${SHORT_PROJECT_ID}_${VERSION}/params/
+  mv ${PROJECT_ID}_${FAMILY_ID}.ped ${OUTPUT_DIR}/${SHORT_PROJECT_ID}_${VERSION}/params/
 
 done