更新 'tasks/TNseq.wdl'

tasks/TNseq.wdl

@@ -27,19 +27,19 @@ task sentieon_TNseq{
         export SENTIEON_LICENSE=${SENTIEON_LICENSE}
         nt=$(nproc)
 
-        #if [${regions}]; then
-        #    INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
-        #else:
+        if [-z "${regions}"]; then
+            INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
+        else:
             INTERVAL=""
-        #fi
+        fi
 
-        #if [${normal_bam}];then
+        if [-z "${normal_bam}"];then
             INPUT="-i ${tumor_bam} -i ${normal_bam}"
             SAMPLE="--tumor_sample ${tumor_name} --normal_sample ${normal_name}"
-        #else:
-        #   INPUT="-i ${tumor_bam}"
-        #   SAMPLE="--tumor_sample ${tumor_name}"
-        #fi
+        else:
+           INPUT="-i ${tumor_bam}"
+           SAMPLE="--tumor_sample ${tumor_name}"
+        fi
 
         sentieon driver -t $nt -r ${ref_dir}/${ref_fasta} \
         $INPUT $INTERVAL \