Improved finding FASTQ files for symlinks and copy to params instead of move

trio_wes_prepare_bcbio_config.sh

@@ -73,27 +73,27 @@ do
 
     # create symlinks for problematic filenames
     mkdir $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE
-    for FILE in `ls $DOWNLOAD_DIR/$PROJECT_ID/raw_data/*/*$SAMPLE*/*_1_*_1.fastq.gz`
+    for FILE in `find $DOWNLOAD_DIR/$ORIG_PROJECT_ID* -wholename "*$SAMPLE*/*_1_*_1.fastq.gz"`
     do
-      newname=`basename $FILE | sed -e 's/_1_/_one_/'`
-      ln -s $FILE $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/${newname%1.fastq.gz}R1.fastq.gz
+	newname=`basename $FILE | sed -e 's/_1_/_one_/'`
+	ln -s $FILE $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/${newname%1.fastq.gz}R1.fastq.gz
     done
-    for FILE in `ls $DOWNLOAD_DIR/$PROJECT_ID/raw_data/*/*$SAMPLE*/*_1_*_2.fastq.gz`
+    for FILE in `find $DOWNLOAD_DIR/$ORIG_PROJECT_ID* -wholename "*$SAMPLE*/*_1_*_2.fastq.gz"`
     do
-      newname=`basename $FILE | sed -e 's/_1_/_one_/'`
-      ln -s $FILE $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/${newname%2.fastq.gz}R2.fastq.gz
+	newname=`basename $FILE | sed -e 's/_1_/_one_/'`
+	ln -s $FILE $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/${newname%2.fastq.gz}R2.fastq.gz
     done
-    for FILE in `ls $DOWNLOAD_DIR/$PROJECT_ID/raw_data/*/*$SAMPLE*/*_2_*_1.fastq.gz`
+    for FILE in `find $DOWNLOAD_DIR/$ORIG_PROJECT_ID* -wholename "*$SAMPLE*/*_2_*_1.fastq.gz"`
     do
-      newname=`basename $FILE | sed -e 's/_2_/_two_/'`
-      ln -s $FILE $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/${newname%1.fastq.gz}R1.fastq.gz
+	newname=`basename $FILE | sed -e 's/_2_/_two_/'`
+	ln -s $FILE $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/${newname%1.fastq.gz}R1.fastq.gz
     done
-    for FILE in `ls $DOWNLOAD_DIR/$PROJECT_ID/raw_data/*/*$SAMPLE*/*_2_*_2.fastq.gz`
+    for FILE in `find $DOWNLOAD_DIR/$ORIG_PROJECT_ID* -wholename "*$SAMPLE*/*_2_*_2.fastq.gz"`
     do
-      newname=`basename $FILE | sed -e 's/_2_/_two_/'`
-      ln -s $FILE $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/${newname%2.fastq.gz}R2.fastq.gz
+	newname=`basename $FILE | sed -e 's/_2_/_two_/'`
+	ln -s $FILE $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/${newname%2.fastq.gz}R2.fastq.gz
     done
-
+    
     for FILE in `ls $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/*_R[1,2].fastq.gz`
     do
       echo "$FILE,$SAMPLE,$FAMILY_ID,$SEX,$PHENOTYPE,$TARGET" >> ${PREFIX}.csv
@@ -117,9 +117,8 @@ do
 
   rm -r ${PREFIX}
 
-  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/
+  cp ${PREFIX}.csv ${OUTPUT_DIR}/${SHORT_PROJECT_ID}_${VERSION}/params/
+  cp ${PROJECT_ID}_${FAMILY_ID}.ped ${OUTPUT_DIR}/${SHORT_PROJECT_ID}_${VERSION}/params/
 
 done