Fixed exclusion of BAM files

submit_trio_wes_archive_project.sh

@@ -17,12 +17,15 @@ source $CONFIG_SH
 cd $OUTPUT_DIR
 
 # Copy bcbio output files
-rsync -av *_$PROJECT_DIR* $ARCHIVE_DIR/
+for family_dir in *_$PROJECT_ID*
+do
+  rsync -av --exclude '*.bam*' $family_dir $ARCHIVE_DIR/
+done
 
 # Copy qc files
 cd qc
 mkdir -p $ARCHIVE_DIR/qc
-rsync -av $PROJECT_DIR* $ARCHIVE_DIR/qc/
+rsync -av $PROJECT_ID* $ARCHIVE_DIR/qc/
 
 # Copy prioritization files
 cd ../prioritization
@@ -32,13 +35,13 @@ DIRS=$(echo $PRIORITY_DIRS | tr ":" "\n")
 
 for dir in $DIRS
 do
-  rsync -av $DIR $ARCHIVE_DIR/prioritization/
+  rsync -av $dir $ARCHIVE_DIR/prioritization/
 done
 
 # move to the archive area and check the md5s
 cd $ARCHIVE_DIR
 
-for family_dir in *_$PROJECT_DIR*
+for family_dir in *_$PROJECT_ID*
 do
   cd $family_dir
   md5sum --check md5sum.txt