Alter: tumor-only

tasks/TNscope.wdl

@@ -41,14 +41,24 @@ task TNscope {
       PON=""
     fi
 
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
-    -r ${ref_dir}/${fasta} $INTERVAL \
-    -i ${tumor_recaled_bam} -i ${normal_recaled_bam} \
+    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} \
+    $INPUT \
+    $INTERVAL \
     --algo TNscope \
-    --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
+    $SAMPLE \
     --dbsnp ${dbsnp_dir}/${dbsnp} \
     $PON \
-    ${sample}.TNscope.TN.vcf
+    ${sample}.TNscope.$typ.vcf
   >>>
 
   runtime {
@@ -59,7 +69,7 @@ task TNscope {
   }
 
   output {
-    File TNscope_vcf= "${sample}.TNscope.TN.vcf"
-    File TNscope_vcf_index = "${sample}.TNscope.TN.vcf.idx"
+    File TNscope_vcf= "${sample}.TNscope.$typ.vcf"
+    File TNscope_vcf_index = "${sample}.TNscope.$typ.vcf.idx"
   }
 }

tasks/TNseq.wdl

@@ -5,8 +5,8 @@ task TNseq {
   String SENTIEON_LICENSE
   File tumor_recaled_bam
   File tumor_recaled_bam_index
-  File normal_recaled_bam
-  File normal_recaled_bam_index
+  File? normal_recaled_bam
+  File? normal_recaled_bam_index
   String tumor_name
   String normal_name
 
@@ -41,31 +41,37 @@ task TNseq {
       PON=""
     fi
 
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
-    -r ${ref_dir}/${fasta} $INTERVAL \
-    -i ${tumor_recaled_bam} -i ${normal_recaled_bam} \
-    --algo TNhaplotyper2 \
-    --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
+    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} \
+    $INPUT $INTERVAL \
+    --algo TNhaplotyper2 $SAMPLE\
     --germline_vcf ${germline_resource} \
     $PON \
-    ${sample}.TNseq.TN.tmp.vcf \
+    ${sample}.TNseq.$typ.vcf \
     --algo OrientationBias --tumor_sample ${tumor_name} \
     ${sample}.orientation \
-    --algo ContaminationModel \
-    --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
+    --algo ContaminationModel $SAMPLE \
     --vcf ${germline_resource} \
     --tumor_segments ${sample}.contamination.segments \
     ${sample}.contamination
     
     ${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 \
+    --algo TNfilter $SAMPLE \
+    -v ${sample}.TNseq.$typ.vcf \
     --contamination ${sample}.contamination \
     --tumor_segments ${sample}.contamination.segments \
     --orientation_priors ${sample}.orientation \
-    ${sample}.TNseq.TN.vcf
+    ${sample}.TNseq.$typ.filter.vcf
   >>>
 
   runtime {
@@ -76,10 +82,10 @@ task TNseq {
   }
 
   output {
-    File TNseq_vcf = "${sample}.TNseq.TN.vcf"
-    File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
-    File TNseq_tmp_vcf = "${sample}.TNseq.TN.tmp.vcf"
-    File TNseq_tmp_vcf_index = "${sample}.TNseq.TN.tmp.vcf.idx"
+    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 contamination = "${sample}.contamination"
     File contamination_segments = "${sample}.contamination.segments"
     File orientation = "${sample}.orientation"

workflow.wdl

@@ -269,7 +269,7 @@ workflow {{ project_name }} {
       if (annovar) {
         call ANNOVAR.ANNOVAR as TNseq_annovar {
           input:
-          vcf=TNseq.TNseq_vcf,
+          vcf=TNseq.TNseq_filter_vcf,
           hg=hg,
           only_pass=only_pass,
           annovar_database=annovar_database,
@@ -282,7 +282,7 @@ workflow {{ project_name }} {
       if (vep) {
         call VEP.VEP as TNseq_VEP {
           input: 
-          vcf=TNseq.TNseq_vcf,
+          vcf=TNseq.TNseq_filter_vcf,
           hg=hg,
           only_pass=only_pass,
           sample_id=sample_id,
@@ -524,7 +524,7 @@ workflow {{ project_name }} {
       if (annovar) {
         call ANNOVAR.ANNOVAR as TNseq_annovar_fb {
           input:
-          vcf=TNseq_fb.TNseq_vcf,
+          vcf=TNseq_fb.TNseq_filter_vcf,
           hg=hg,
           only_pass=only_pass,
           annovar_database=annovar_database,
@@ -537,7 +537,7 @@ workflow {{ project_name }} {
       if (vep) {
         call VEP.VEP as TNseq_VEP_fb {
           input: 
-          vcf=TNseq_fb.TNseq_vcf,
+          vcf=TNseq_fb.TNseq_filter_vcf,
           hg=hg,
           only_pass=only_pass,
           sample_id=sample_id,