Fix bug: TNseq.wdl

tasks/TNseq.wdl

@@ -60,7 +60,7 @@ task TNseq {
     --tumor_segments ${sample}.contamination.segments \
     ${sample}.contamination
     
-    sentieon driver -r REFERENCE \
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r REFERENCE \
     --algo TNfilter \
     --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
     -v ${sample}.TNseq.TN.tmp.vcf \
@@ -78,10 +78,10 @@ task TNseq {
   }
 
   output {
-    File TNseq_vcf = "${sample}.TNseq.TN.vcf"
-    File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
     File contamination = "${sample}.contamination"
     File contamination_segments = "${sample}.contamination.segments"
     File orientation = "${sample}.orientation"
+    File TNseq_vcf = "${sample}.TNseq.TN.vcf"
+    File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
   }
 }