Fix combine step with many sc files (#74)

* Fix combine step with many sc files

Using find

Author: mjz1

src/scripts/Cicero.sh

@@ -315,8 +315,8 @@ parallel --joblog 02_Cicero.log $PARALLEL_ARG < cmds-02.sh
 #########################
 echo "Step 03 - $(date +'%Y.%m.%d %H:%M:%S') - Combine"
 {
-cat $CICERO_DATADIR/$SAMPLE/*/unfiltered.fusion.txt | sort -V -k 9,9 -k 10,10n -k 11,11n > $CICERO_DATADIR/$SAMPLE/unfiltered.fusion.txt
-cat $CICERO_DATADIR/$SAMPLE/*/unfiltered.internal.txt | sort -V -k 9,9 -k 10,10n -k 11,11n > $CICERO_DATADIR/$SAMPLE/unfiltered.internal.txt
+find $CICERO_DATADIR/$SAMPLE/*/ -type f -name 'unfiltered.fusion.txt' -exec cat {} \; | sort -V -k 9,9 -k 10,10n -k 11,11n > $CICERO_DATADIR/$SAMPLE/unfiltered.fusion.txt
+find $CICERO_DATADIR/$SAMPLE/*/ -type f -name 'unfiltered.internal.txt' -exec cat {} \; | sort -V -k 9,9 -k 10,10n -k 11,11n > $CICERO_DATADIR/$SAMPLE/unfiltered.internal.txt
 } 1> 03_Combine.out 2> 03_Combine.err
 
 ## QC
@@ -384,4 +384,3 @@ fi
 ### Blow away tmp configs ###
 #############################
 #rm -rf $SJ_CONFIGS
-