update star fusion

alignment/starfusion.sh

@@ -50,14 +50,14 @@ then
     fi 
     export TMP_HOME=$tmphome
     index_path=${refgeno}/CTAT_lib_trinity/
-    trinity /usr/local/src/STAR-Fusion/STAR-Fusion --min_sum_frags 3 --CPU $SLURM_CPUS_ON_NODE --genome_lib_dir ${index_path} --left_fq ${fq1} --right_fq ${fq2} --examine_coding_effect --output_dir star_fusion
-    cp star_fusion/star-fusion.fusion_predictions.abridged.tsv ${pair_id}.starfusion.txt
-    cp star_fusion/star-fusion.fusion_predictions.abridged.coding_effect.tsv ${pair_id}.starfusion.coding_effect.txt
+    trinity /usr/local/src/STAR-Fusion/STAR-Fusion --min_sum_frags 3 --CPU $SLURM_CPUS_ON_NODE --genome_lib_dir ${index_path} --left_fq ${fq1} --right_fq ${fq2} --examine_coding_effect --output_dir ${pair_id}_star_fusion
+    cp ${pair_id}_star_fusion/star-fusion.fusion_predictions.abridged.tsv ${pair_id}.starfusion.txt
+    cp ${pair_id}_star_fusion/star-fusion.fusion_predictions.abridged.coding_effect.tsv ${pair_id}.starfusion.coding_effect.txt
 else
     module add star/2.5.2b
     index_path=${refgeno}/CTAT_lib/
-    STAR-Fusion --genome_lib_dir ${index_path} --min_sum_frags 3 --left_fq ${fq1} --right_fq ${fq2} --output_dir star_fusion &> star_fusion.err
-    cp star_fusion/star-fusion.fusion_candidates.final.abridged ${pair_id}.starfusion.txt
+    STAR-Fusion --genome_lib_dir ${index_path} --min_sum_frags 3 --left_fq ${fq1} --right_fq ${fq2} --output_dir ${pair_id}_star_fusion &> star_fusion.err
+    cp ${pair_id}_star_fusion/star-fusion.fusion_candidates.final.abridged ${pair_id}.starfusion.txt
 fi
 if [[ $filter==1 ]]
 then