print starfusion

alignment/starfusion.sh

@@ -41,7 +41,8 @@ baseDir="`dirname \"$0\"`"
 source /etc/profile.d/modules.sh
 module add python/2.7.x-anaconda star/2.5.2b bedtools/2.26.0
 
-if [[ $method == 'trinity' ]]
+
+if [[ -n $method ]] && [[ $method == 'trinity' ]]
 then
     module load trinity/1.6.0
     tmphome="/tmp/$USER"
@@ -58,7 +59,7 @@ then
     cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "singularity exec /project/shared/bicf_workflow_ref/singularity_images/agfusion.simg agfusion annotate  -db  /project/shared/bicf_workflow_ref/singularity_images/pyensembl/GRCh38/ensembl92/agfusion.homo_sapiens.92.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
 else
     refgeno=${index_path}/CTAT_resource_lib
-    STAR-Fusion --genome_lib_dir ${refgeno} --min_sum_frags 3 --left_fq ${fq1} --right_fq ${fq2} --output_dir ${pair_id}_star_fusion &> star_fusion.err
+    STAR-Fusion --genome_lib_dir ${refgeno} --min_sum_frags 3 --left_fq ${fq1} --right_fq ${fq2} --output_dir ${pair_id}_star_fusion
     cp ${pair_id}_star_fusion/star-fusion.fusion_candidates.final.abridged ${pair_id}.starfusion.txt
     cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "agfusion annotate  -db agfusion.homo_sapiens.95.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
 fi