Intragenic fusion parsing added to container used in OncoKB processes.

Author: kevinmhadi

bin/oncokb/process_singularity.sh

@@ -177,17 +177,31 @@ fi
 
 if [ -e ${FUSIONS} ] && [ ! $(wc -c <${FUSIONS}) == 0 ]; then
 
-        # Below must be inside parentheses so the environment change happens within a subshell
-        (
-            Rscript ${HOME}/scripts/parse_fusions_for_oncokb.R --libdir ${LIBDIR} --fusions ${FUSIONS} --path ./input_fusions.tsv
-        )
+        
+        Rscript ${HOME}/scripts/parse_fusions_for_oncokb.R --libdir ${LIBDIR} --fusions ${FUSIONS} --path ./input_fusions.tsv
+        
         set -x
         python ${HOME}/git/oncokb-annotator/FusionAnnotator.py \
             -i ./input_fusions.tsv \
             -o ./oncokb_fusions.tsv \
             $( test ! $(tolower ${TUMOR_TYPE}) = unknown && printf %s "-t ${TUMOR_TYPE}" )  \
             -b $ONCOKB_TOKEN \
             -d
+        
+        python ${HOME}/git/oncokb-annotator/MafAnnotator.py \
+            -i ./partial_tandem_duplication.maf \
+            -o ./oncokb_partial_tandem_duplication.tsv \
+            $( test ! $(tolower ${TUMOR_TYPE}) = unknown && printf %s "-t ${TUMOR_TYPE}" )  \
+            -b $ONCOKB_TOKEN \
+            -d \
+            -a
+        
+        python ${HOME}/git/oncokb-annotator/StructuralVariantAnnotator.py \
+            -i ./intragenic_del.tsv \
+            -o ./oncokb_intragenic_del.tsv \
+            $( test ! $(tolower ${TUMOR_TYPE}) = unknown && printf %s "-t ${TUMOR_TYPE}" )  \
+            -b $ONCOKB_TOKEN \
+            -d
         set +x
 
         Rscript ${HOME}/scripts/add_fusion_metadata_to_oncokb.R \

modules/local/oncokb/main.nf

@@ -12,8 +12,8 @@ process ONCOKB_ANNOTATOR {
     //     'mskilab/unified:0.0.12' }"
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://mskilab/unified:0.0.28-rebuild':
-        'mskilab/unified:0.0.28-rebuild' }"
+        'docker://mskilab/unified:0.0.29-rebuild':
+        'mskilab/unified:0.0.29-rebuild' }"
 
     input:
     tuple val(meta), path(vcf), path(fusions), path(cna)
@@ -26,6 +26,11 @@ process ONCOKB_ANNOTATOR {
     output:
     path "merged_oncokb.maf", emit: merged_oncokb_vcf
     path "merged_oncokb_fusions.tsv", emit: merged_oncokb_fusions
+    path "merged_oncokb_fusions.json", emit: merged_oncokb_fusions_json, optional: true
+    path "merged_oncokb_intragenic_del.tsv", emit: merged_oncokb_intragenic_del
+    path "merged_oncokb_intragenic_del.json", emit: merged_oncokb_intragenic_del_json, optional: true
+    path "merged_oncokb_partial_tandem_duplication.tsv", emit: merged_oncokb_partial_tandem_duplication
+    path "merged_oncokb_partial_tandem_duplication.json", emit: merged_oncokb_partial_tandem_duplication_json, optional: true
     path "merged_oncokb_cna.tsv", emit: merged_oncokb_cna
     path "versions.yml",      emit: versions