file name locations

alignment/filter_genefusions.pl

@@ -6,7 +6,7 @@ use Getopt::Long qw(:config no_ignore_case no_auto_abbrev);
 my %opt = ();
 my $results = GetOptions (\%opt,'fusion|f=s','prefix|p=s','help|h');
 my %entrez;
-open ENT, "</project/shared/bicf_workflow_ref/gene_info.human.txt" or die $!;
+open ENT, "</project/shared/bicf_workflow_ref/human/gene_info.human.txt" or die $!;
 my $headline = <ENT>;
 while (my $line = <ENT>) {
   chomp($line);

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/2.6.0
+module load singularity/2.6.1
 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
 

genect_rnaseq/cBioPortal_documents.pl

@@ -6,7 +6,7 @@ use File::Basename;
 
 my $results= GetOptions (\%opt,'fpkm|f=s','logcpm|l=s','cnv|c=s','prefix|p=s','help|h');
 
-open ENT_ENS, "</project/shared/bicf_workflow_ref/gene_info.human.txt" or die $!;
+open ENT_ENS, "</project/shared/bicf_workflow_ref/human/gene_info.human.txt" or die $!;
 my %entrez;
 my $ent_header = <ENT_ENS>;
 while (my $line = <ENT_ENS>){
@@ -24,7 +24,7 @@ while (my $line = <ENT_ENS>){
   $entrez{$row[3]}=$entrez{$row[4]};
 }
 close ENT_ENS;
-open ENT_ENS, "</project/shared/bicf_workflow_ref/gene2ensembl.human.txt" or die $!;
+open ENT_ENS, "</project/shared/bicf_workflow_ref/human/gene2ensembl.human.txt" or die $!;
 my $ens_header = <ENT_ENS>;
 while (my $line = <ENT_ENS>){
   chomp $line;