fix: rm germline source

tasks/TNseq.wdl

@@ -71,6 +71,10 @@ task TNseq {
     --algo TNfilter $SAMPLE \
     -v ${sample}.TNseq.raw.vcf \
     ${sample}.TNseq.vcf
+
+    touch ${sample}.contamination
+    touch ${sample}.contamination.segments
+    touch ${sample}.orientation
   >>>
   
   runtime {
@@ -81,6 +85,8 @@ task TNseq {
   }
   
   output {
+    File raw_vcf = "${sample}.TNseq.raw.vcf"
+    File raw_vcf_index = "${sample}.TNseq.raw.vcf.idx"
     File vcf = "${sample}.TNseq.vcf"
     File vcf_index = "${sample}.TNseq.vcf.idx"
     File contamination = "${sample}.contamination"