diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh index a3a509907dfc292e9e2d8f203ca938477defb060..2b26813fab2b5e77104df818b157b2918f15b3b4 100644 --- a/alignment/starfusion.sh +++ b/alignment/starfusion.sh @@ -58,10 +58,11 @@ then 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"_"$9}' |grep -v 'LeftGene' |sh else + export PYENSEMBL_CACHE_DIR=/opt refgeno=${index_path}/CTAT_resource_lib STAR-Fusion --genome_lib_dir ${refgeno} --min_sum_frags 3 --CPU $NPROC --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 - 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 + cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "agfusion annotate -db /usr/local/src/agfusion.homo_sapiens.95.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh fi if [[ $filter == 1 ]]