feat: html report

.tests/integration/config.yaml

@@ -4,7 +4,7 @@ aligner: "bwa_gpu"
 
 modules:
   alignment: "906d25d0d4791eb5a54cba9954fddf29e27b85dd"
-  annotation: "e58432c3467db31621ab51a16034a026cf2a2c84"
+  annotation: "3a05574"
   cnv_sv: "v0.4.1"
   compression: "v1.1.0"
   filtering: "b7f4dc3"
@@ -14,6 +14,7 @@ modules:
   qc: "v0.3.0"
   misc: "v0.1.0"
   sentieon: "develop"
+  reports: "7c8b8c5"
 
 default_container: "docker://hydragenetics/common:0.1.9"
 
@@ -27,9 +28,14 @@ reference:
   wgs_intervals: "reference/wgs.interval_list"
   design_intervals: "reference/wgs.interval_list" #HSMetrics
   design_intervals_gatk_cnv: "reference/wgs.interval_list"
+  skip_chrs:
+    - chrM
 
 trimmer_software: "fastp_pe"
 
+annotate_cnv:
+  cna_exons: "reference/hg38_CNA.bed" 
+
 arriba:
   assembly: "reference/assembly.fasta"
   blacklist: "reference/arriba_blacklist.txt"
@@ -62,6 +68,13 @@ cnvkit_table:
 cnvkit_vcf:
   container: "docker://python:3.9.9-slim-buster"
 
+cnv_html_report:
+  show_table: true
+  template_dir: "../../config/cnv_report_template"
+  cnv_vcf:
+    - annotation: cna_exons
+      filter: cnv_hardfilter
+
 crumble:
   container: "docker://hydragenetics/crumble:0.8.3"
   extra: "-O CRAM"
@@ -74,9 +87,10 @@ fastqc:
 
 filter_vcf:
   germline: "../../config/config_germline_filter.yaml"
+  cnv_hardfilter: "/../../config_cnv_hardfilter.yaml"
 
 fusioncatcher:
-  genome_path: "reference/"
+  genome_path: "reference"
 
 gatk_cnv_collect_allelic_counts:
   container: "docker://hydragenetics/gatk4:4.2.2.0"

.tests/integration/reference/hg38_CNA.bed

@@ -0,0 +1 @@
+