fix: rm germline source

tasks/TNseq.wdl

@@ -40,25 +40,36 @@ task TNseq {
       SAMPLE="--tumor_sample ${tumor_name}"
     fi
     
+    # sentieon driver -t $nt -r ${ref_dir}/${fasta} \
+    # $INPUT $INTERVAL \
+    # --algo TNhaplotyper2 $SAMPLE \
+    # --germline_vcf ${germline_resource} \
+    # ${sample}.TNseq.raw.vcf \
+    # --algo OrientationBias --tumor_sample ${tumor_name} \
+    # ${sample}.orientation \
+    # --algo ContaminationModel $SAMPLE \
+    # --vcf ${germline_resource} \
+    # --tumor_segments ${sample}.contamination.segments \
+    # ${sample}.contamination
+    
+    # sentieon driver -t $nt \
+    # -r ${ref_dir}/${fasta} \
+    # --algo TNfilter $SAMPLE \
+    # -v ${sample}.TNseq.raw.vcf \
+    # --contamination ${sample}.contamination \
+    # --tumor_segments ${sample}.contamination.segments \
+    # --orientation_priors ${sample}.orientation \
+    # ${sample}.TNseq.vcf
+
     sentieon driver -t $nt -r ${ref_dir}/${fasta} \
     $INPUT $INTERVAL \
     --algo TNhaplotyper2 $SAMPLE \
-    --germline_vcf ${germline_resource} \
-    ${sample}.TNseq.raw.vcf \
-    --algo OrientationBias --tumor_sample ${tumor_name} \
-    ${sample}.orientation \
-    --algo ContaminationModel $SAMPLE \
-    --vcf ${germline_resource} \
-    --tumor_segments ${sample}.contamination.segments \
-    ${sample}.contamination
+    ${sample}.TNseq.raw.vcf
     
     sentieon driver -t $nt \
     -r ${ref_dir}/${fasta} \
     --algo TNfilter $SAMPLE \
     -v ${sample}.TNseq.raw.vcf \
-    --contamination ${sample}.contamination \
-    --tumor_segments ${sample}.contamination.segments \
-    --orientation_priors ${sample}.orientation \
     ${sample}.TNseq.vcf
   >>>
   

workflow.wdl

@@ -88,8 +88,6 @@ workflow {{ project_name }} {
     tumor_name=sample_id + ".T",
     fasta=fasta,
     ref_dir=ref_dir,
-    dbsnp=dbsnp,
-    dbsnp_dir=dbsnp_dir,
     regions=regions,
     interval_padding=interval_padding,
     germline_resource=germline_resource,