Merge pull request #477 from genomic-medicine-sweden/add_cytobands

feat: add cytobands to cnv report

.tests/integration/DATA/centromeres.bed

@@ -0,0 +1,2 @@
+chrA	2500	2600	centromere
+chrB	3450	3550	centromere

.tests/integration/config/config.yaml

@@ -150,6 +150,7 @@ merge_cnv_json:
     - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_amp_genes.vcf.gz
     - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_loh_genes_all.vcf.gz
   germline_vcf: snv_indels/bcbio_variation_recall_ensemble/{sample}_{type}.ensembled.vep_annotated.filter.germline.exclude.blacklist.vcf.gz
+  cytobands: "DATA/centromeres.bed"
 
 purecn:  
   normaldb: "reference/purecn_dummy_normaldb.rds"

config/config.data.hg19.yaml

@@ -125,6 +125,7 @@ merge_cnv_json:
   annotations:
     - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_240307.bed"
     - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes.bed"
+  cytobands: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cytoBand.hg19.txt"
 
 mosdepth:
   extra: "--no-per-base --fast-mode"

config/config.data.hg38.yaml

@@ -125,6 +125,7 @@ merge_cnv_json:
   annotations:
     - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_hg38.bed"
     - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes_hg38.bed"
+  cytobands: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cytoBand.hg38.txt"
 
 mosdepth:
   extra: "--no-per-base --fast-mode"

config/config.yaml

@@ -73,7 +73,7 @@ cnvkit_scatter:
 
 cnv_html_report:
   show_table: true
-  show_cytobands: true
+  cytobands: true
   extra_tables:
     - name: Small CNVs and 1p19q
       description: >
@@ -206,10 +206,10 @@ merge_cnv_json:
   filtered_cnv_vcfs:
     - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_amp_genes.filter.cnv_hard_filter_amp.vcf.gz
     - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_loh_genes_all.filter.cnv_hard_filter_loh.vcf.gz
+  germline_vcf: snv_indels/bcbio_variation_recall_ensemble/{sample}_{type}.ensembled.vep_annotated.filter.germline.exclude.blacklist.vcf.gz
   unfiltered_cnv_vcfs:
     - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_amp_genes.vcf.gz
     - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_loh_genes_all.vcf.gz
-  germline_vcf: snv_indels/bcbio_variation_recall_ensemble/{sample}_{type}.ensembled.vep_annotated.filter.germline.exclude.blacklist.vcf.gz
 
 mosdepth:
   container: "docker://hydragenetics/mosdepth:0.3.2"

config/references/design_files.hg19.yaml

@@ -152,6 +152,13 @@
      type: file        
      url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.1/design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.210608.bed.gz.tbi
 
+ merge_cnv_json:
+   cytobands:
+     checksum: 64de0499795484f1b70410a4cdd3d06f
+     path: GMS560/cnv/cytoBand.hg19.txt
+     type: file
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.9.0/cnv/cytoBand.hg19.txt
+
  purecn:    
    intervals: 
      checksum: 0857e05962696cd3c2e5a4ea94d0fb2c

config/references/design_files.hg38.yaml

@@ -145,6 +145,13 @@
      type: file        
      url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz.tbi
 
+ merge_cnv_json:
+   cytobands:
+     checksum: 1b87bbfe572064c2a40d79683ea7a6ad
+     path: GMS560/cnv/cytoBand.hg38.txt
+     type: file
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.9.0/cnv/cytoBand.hg38.txt
+
  purecn:    
    intervals: 
      checksum: 868c8991360482315f820ae822108965

workflow/Snakefile

@@ -639,11 +639,11 @@ use rule cnv_html_report from reports as reports_cnv_html_report with:
         tc_file=get_tc_file,
         extra_table_files=[t["path"] for t in config.get("cnv_html_report", {}).get("extra_tables", [])],
     params:
+        extra_tables=config.get("cnv_html_report", {}).get("extra_tables", []),
         include_table=config.get("cnv_html_report", {}).get("show_table", True),
-        include_cytobands=config.get("cnv_html_report", {}).get("show_cytobands", True),
+        include_cytobands=config.get("cnv_html_report", {}).get("cytobands", True),
         tc=get_tc,
         tc_method=lambda wildcards: wildcards.tc_method,
-        extra_tables=config.get("cnv_html_report", {}).get("extra_tables", []),
 
 
 module misc: