fixed tophat output naming

tools/tophat

@@ -18,24 +18,24 @@ PART=$5
 COMMON_NAME=$6
 
 # make sure we have empty output files in case of errors
-touch $COMMON_NAME-out.txt
-touch $COMMON_NAME-accepted_hits.bam
-touch $COMMON_NAME-align_summary.txt
+touch $BASE_NAME-$COMMON_NAME-out.txt
+touch $BASE_NAME-$COMMON_NAME-accepted_hits.bam
+touch $BASE_NAME-$COMMON_NAME-align_summary.txt
 
 java -Xmx512m \
      -jar trimmomatic-0.36.jar PE -threads 1 -phred33 \
-     forward-$COMMON_NAME reverse-$COMMON_NAME \
+     $BASE_NAME-forward-$COMMON_NAME $BASE_NAME-reverse-$COMMON_NAME \
      left_result.paired_trim.forward_$COMMON_NAME.fastq left_result.unpaired_trim.forward_$COMMON_NAME.fastq \
      right_result.paired_trim.reverse_$COMMON_NAME.fastq right_result.unpaired_trim.reverse_$COMMON_NAME.fastq \
      ILLUMINACLIP:fasta_adapter.txt:2:40:15 LEADING:3 TRAILING:6 SLIDINGWINDOW:4:15 MINLEN:50 \
-     2>&1 | tee $COMMON_NAME-trimmomatic.txt
+     2>&1 | tee $BASE_NAME-$COMMON_NAME-trimmomatic.txt
 
 # empty outputs?
 LEFT_SIZE=`ls -l left_result.paired_trim.forward_$COMMON_NAME.fastq | cut -d ' ' -f 5`
 RIGHT_SIZE=`ls -l right_result.paired_trim.reverse_$COMMON_NAME.fastq | cut -d ' ' -f 5`
 if [ $LEFT_SIZE -lt 50 -o $RIGHT_SIZE -lt 50 ]; then
     echo "Warning: trimmomatic output was 0 sequences"
-    touch $COMMON_NAME-accepted_hits.bam
+    touch $BASE_NAME-$COMMON_NAME-accepted_hits.bam
     exit 0
 fi
 
@@ -47,13 +47,13 @@ tophat2 --no-coverage-search --no-novel-juncs --no-novel-indels --no-coverage-se
         --transcriptome-index=transcriptome_data/$REF_PREFIX -o work-$$ ./$REF_PREFIX \
         left_result.paired_trim.forward_$COMMON_NAME.fastq \
         right_result.paired_trim.reverse_$COMMON_NAME.fastq \
-        | tee $COMMON_NAME-out.txt
+        | tee $BASE_NAME-$COMMON_NAME-out.txt
 
 echo
 find work-$$
 echo
 
 # we only need the accepted hits, but it needs a unique name
-mv work-$$/accepted_hits.bam $COMMON_NAME-accepted_hits.bam
-mv work-$$/align_summary.txt $COMMON_NAME-align_summary.txt
+mv work-$$/accepted_hits.bam $BASE_NAME-$COMMON_NAME-accepted_hits.bam
+mv work-$$/align_summary.txt $BASE_NAME-$COMMON_NAME-align_summary.txt