Fixbug: remove

tasks/TNscope.wdl

@@ -44,11 +44,9 @@ task TNscope {
     if [ ${normal_recaled_bam} ]; then
       INPUT="-i ${tumor_recaled_bam} -i ${normal_recaled_bam}"
       SAMPLE="--tumor_sample ${tumor_name} --normal_sample ${normal_name}"
-      typ="TN"
     else
       INPUT="-i ${tumor_recaled_bam}"
       SAMPLE="--tumor_sample ${tumor_name}"
-      typ="T"
     fi
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} \
@@ -58,7 +56,7 @@ task TNscope {
     $SAMPLE \
     --dbsnp ${dbsnp_dir}/${dbsnp} \
     $PON \
-    ${sample}.TNscope.$typ.vcf
+    ${sample}.TNscope.vcf
   >>>
 
   runtime {
@@ -69,7 +67,7 @@ task TNscope {
   }
 
   output {
-    File TNscope_vcf= "${sample}.TNscope.$typ.vcf"
-    File TNscope_vcf_index = "${sample}.TNscope.$typ.vcf.idx"
+    File TNscope_vcf= "${sample}.TNscope.vcf"
+    File TNscope_vcf_index = "${sample}.TNscope.vcf.idx"
   }
 }

tasks/TNseq.wdl

@@ -44,11 +44,9 @@ task TNseq {
     if [ ${normal_recaled_bam} ]; then
       INPUT="-i ${tumor_recaled_bam} -i ${normal_recaled_bam}"
       SAMPLE="--tumor_sample ${tumor_name} --normal_sample ${normal_name}"
-      typ="TN"
     else
       INPUT="-i ${tumor_recaled_bam}"
       SAMPLE="--tumor_sample ${tumor_name}"
-      typ="T"
     fi
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} \
@@ -56,7 +54,7 @@ task TNseq {
     --algo TNhaplotyper2 $SAMPLE \
     --germline_vcf ${germline_resource} \
     $PON \
-    ${sample}.TNseq.$typ.vcf \
+    ${sample}.TNseq.vcf \
     --algo OrientationBias --tumor_sample ${tumor_name} \
     ${sample}.orientation \
     --algo ContaminationModel $SAMPLE \
@@ -67,11 +65,11 @@ task TNseq {
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
     -r ${ref_dir}/${fasta} \
     --algo TNfilter $SAMPLE \
-    -v ${sample}.TNseq.$typ.vcf \
+    -v ${sample}.TNseq.vcf \
     --contamination ${sample}.contamination \
     --tumor_segments ${sample}.contamination.segments \
     --orientation_priors ${sample}.orientation \
-    ${sample}.TNseq.$typ.filter.vcf
+    ${sample}.TNseq.filter.vcf
   >>>
 
   runtime {
@@ -82,10 +80,10 @@ task TNseq {
   }
 
   output {
-    File TNseq_filter_vcf='${sample}.TNseq.$typ.filter.vcf'
-    File TNseq_filter_vcf_index = "${sample}.TNseq.$typ.filter.vcf.idx"
-    File TNseq_vcf = "${sample}.TNseq.$typ.vcf"
-    File TNseq_vcf_index = "${sample}.TNseq.$typ.vcf.idx"
+    File TNseq_filter_vcf='${sample}.TNseq.filter.vcf'
+    File TNseq_filter_vcf_index = "${sample}.TNseq.filter.vcf.idx"
+    File TNseq_vcf = "${sample}.TNseq.vcf"
+    File TNseq_vcf_index = "${sample}.TNseq.vcf.idx"
     File contamination = "${sample}.contamination"
     File contamination_segments = "${sample}.contamination.segments"
     File orientation = "${sample}.orientation"