feat: germline source

defaults

@@ -13,8 +13,8 @@
   "dbsnp": "dbsnp_138.hg19_nochr_sorted.vcf",
   "annovar_database": "oss://genomics-platform-reference-data/annovar/",
   "annotsv_database": "oss://ivd-product/reference/AnnotSV/",
-  "germline_resource": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz",
-  "germline_resource_tbi": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",
+  "germline_resource": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.raw.sites.vcf",
+  "germline_resource_tbi": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.raw.sites.vcf.idx",
   "gc": "oss://ivd-product/reference/Sequenza/GRCh38.gc50Base.wig.gz",
   "baseline": "oss://ivd-product/reference/MSIsensor/hg38_reference.list_baseline",
   "fastq_screen_conf": "oss://genomics-platform-reference-data/fastq_screen_reference/fastq_screen.conf",

tasks/TNseq.wdl

@@ -40,41 +40,41 @@ 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 \
-    ${sample}.TNseq.raw.vcf
+    --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
 
-    touch ${sample}.contamination
-    touch ${sample}.contamination.segments
-    touch ${sample}.orientation
+    # sentieon driver -t $nt -r ${ref_dir}/${fasta} \
+    # $INPUT $INTERVAL \
+    # --algo TNhaplotyper2 $SAMPLE \
+    # ${sample}.TNseq.raw.vcf
+    
+    # sentieon driver -t $nt \
+    # -r ${ref_dir}/${fasta} \
+    # --algo TNfilter $SAMPLE \
+    # -v ${sample}.TNseq.raw.vcf \
+    # ${sample}.TNseq.vcf
+
+    # touch ${sample}.contamination
+    # touch ${sample}.contamination.segments
+    # touch ${sample}.orientation
   >>>
   
   runtime {