Add structural variants summary and update file names in main workflow

Author: anand-imcm

README.md

@@ -74,6 +74,7 @@ The main output files are listed below:
   - `PASS_norm_phased_variants_summary`: List of variants (tab delimited text).
   - `PASS_norm_phased_ontarget_variants_summary`: List of on-target variants (tab delimited text).
   - `PASS_norm_phased_annotated_ontarget_variants_vcf`: VCF file containing annotated on-target variants (vcf).
+  - `Structural_PASS_norm_variants_summary`: List of structural variants (tab delimited text).
   - `coverage_depth_plot`: Plot of coverage depth (png).
   - `variants_summary`: Summary of all variants (tab delimited text).
   - `variants_vaf_gt0.5_summary`: Summary of all variants after filtering by variant allele fraction (VAF<0.5) (tab delimited text).

workflows/main.wdl

@@ -77,10 +77,12 @@ workflow main {
         File raw_hifi_to_reference_alignment_PASS_norm_phased_variants_vep_stats = AnnotateVariants.raw_hifi_to_reference_alignment_PASS_norm_phased_variants_vep_stats
 
         File raw_hifi_to_reference_alignment_PASS_norm_phased_variants_summary = Summary.raw_hifi_to_reference_alignment_PASS_norm_phased_variants_summary
+        File raw_hifi_to_reference_alignment_PASS_norm_phased_annotated_ontarget_variants_vcf = Summary.raw_hifi_to_reference_alignment_PASS_norm_phased_annotated_ontarget_variants
         File raw_hifi_to_reference_alignment_PASS_norm_phased_ontarget_variants_summary = Summary.raw_hifi_to_reference_alignment_PASS_norm_phased_ontarget_variants_summary
-        File raw_hifi_to_reference_alignment_PASS_norm_phased_annotated_ontarget_variants_vcf = Summary.raw_hifi_to_reference_alignment_PASS_norm_phased_annotated_ontarget_variants  
+        File raw_hifi_to_reference_alignment_structural_PASS_norm_variants_summary = Summary.raw_hifi_to_reference_alignment_structural_PASS_norm_variants_summary
         File? coverage_depth_plot = Summary.coverage_depth_plot
         File variants_summary = Summary.variants_summary
+        File variants_vaf_gt0_5_summary = Summary.variants_vaf_gt0_5_summary
         File sequence_summary = Summary.sequence_summary
     }