new

tasks/starfusion.wdl

@@ -23,7 +23,15 @@ task starfusion{
             --FusionInspector validate \
             --examine_coding_effect
 
-
+        mv  ${sample_id}/output/star-fusion.fusion_predictions.tsv ${sample_id}/output/${sample_id}_star-fusion.fusion_predictions.tsv
+        mv  ${sample_id}/output/star-fusion.fusion_predictions.abridged.tsv ${sample_id}/output/${sample_id}_star-fusion.fusion_predictions.abridged.tsv
+        mv  ${sample_id}/output/star-fusion.fusion_predictions.abridged.coding_effect.tsv ${sample_id}/output/${sample_id}_star-fusion.fusion_predictions.abridged.coding_effect.tsv
+       
+        cp  ${sample_id}/output/FusionInspector-validate/finspector.FusionInspector.fusions.tsv ${sample_id}/output/${sample_id}_finspector.FusionInspector.fusions.tsv
+        cp  ${sample_id}/output/FusionInspector-validate/finspector.FusionInspector.fusions.abridged.tsv ${sample_id}/output/${sample_id}_finspector.FusionInspector.fusions.abridged.tsv
+        cp  ${sample_id}/output/FusionInspector-validate/finspector.FusionInspector.fusions.abridged.tsv.annotated ${sample_id}/output/${sample_id}_finspector.FusionInspector.fusions.abridged.tsv.annotated
+        cp  ${sample_id}/output/FusionInspector-validate/finspector.FusionInspector.fusions.abridged.tsv.annotated.coding_effect ${sample_id}/output/${sample_id}_finspector.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
+        cp  ${sample_id}/output/FusionInspector-validate/finspector.fusion_inspector_web.html ${sample_id}/output/${sample_id}_finspector.fusion_inspector_web.html
         tar -zcvf ${sample_id}/output/${sample_id}_FusionInspector-validate.tgz ${sample_id}/output/FusionInspector-validate
 
     >>>
@@ -36,10 +44,8 @@ task starfusion{
     }
 
     output {
-        Array[File] starfusion_result=glob("${sample_id}/output/*.tsv")
-        Array[File] starfusion_bam=glob("${sample_id}/output/*.bam")
-        Array[File] starfusion_tab=glob("${sample_id}/output/*.tab")
-        Array[File] starfusion_junction=glob("${sample_id}/output/*.junction")
+        Array[File] starfusion_result=glob("${sample_id}/output/${sample_id}_star-fusion*")
+        Array[File] finspector_result=glob("${sample_id}/output/${sample_id}_finspector*")
         Array[File] starfusion_out=glob("${sample_id}/output/*.out")
         Array[File] starfusion_tgz=glob("${sample_id}/output/*.tgz")
     }