update agfusion

alignment/filter_genefusions.pl

@@ -29,6 +29,8 @@ while (my $line = <OM>) {
 my @exonfiles = `ls */*.exons.txt`;
 foreach $efile (@exonfiles) {
     chomp($efile);
+    my @leftexons;
+    my @rightexons;
     my ($dir,$pair,@etc) = split(/\/|\./,$efile);
     open EFILE, "<$efile" or die $!;
     my $header = <EFILE>;

alignment/starfusion.sh

@@ -60,7 +60,7 @@ else
     cp ${pair_id}_star_fusion/star-fusion.fusion_candidates.final.abridged ${pair_id}.starfusion.txt
 fi
 
-module load singularity/2.6.1
+module load singularity/3.0.2
 export PYENSEMBL_CACHE_DIR="/project/shared/bicf_workflow_ref/singularity_images"
 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