Fix bug: TNseq.wdl

tasks/TNseq.wdl

@@ -60,7 +60,8 @@ task TNseq {
     --tumor_segments ${sample}.contamination.segments \
     ${sample}.contamination
     
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r REFERENCE \
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} \
     --algo TNfilter \
     --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
     -v ${sample}.TNseq.TN.tmp.vcf \