Add cytobands to inputs

Author: VJalili

src/sv_shell/gather_batch_evidence.sh

@@ -186,6 +186,7 @@ cnmops_inputs_json="$(realpath "${output_dir}/cnmops_inputs.json")"
 cnmops_outputs_json="$(realpath "${output_dir}/cnmops_outputs.json")"
 
 jq -n \
+  --slurpfile inputs "${input_json}" \
   --arg r1 "3" \
   --arg r2 "10" \
   --arg batch "${batch}" \
@@ -213,7 +214,8 @@ jq -n \
       "allo_file": $allo_file,
       "ref_dict": $ref_dict,
       "prefix": $prefix,
-      "stitch_and_clean_large_events": $stitch_and_clean_large_events
+      "stitch_and_clean_large_events": $stitch_and_clean_large_events,
+      "cytobands": $inputs[0].cytobands
   }' > "${cnmops_inputs_json}"
 
 bash /opt/sv_shell/cnmops.sh "${cnmops_inputs_json}" "${cnmops_outputs_json}"

src/sv_shell/sample_inputs/gather_batch_evidence.json

@@ -520,5 +520,6 @@
   "wham_vcfs": [
     "/inputs/NA12878.wham.vcf.gz"
   ],
-  "min_svsize": 50
+  "min_svsize": 50,
+  "cytobands": "/inputs/cytobands_hg38.bed.gz"
 }

src/sv_shell/single_sample_pipeline.sh

@@ -319,7 +319,8 @@ jq -n \
       run_module_metrics: $inputs[0].run_batchevidence_metrics,
       median_cov_mem_gb_per_sample: $inputs[0].median_cov_mem_gb_per_sample,
       ref_panel_median_cov: $inputs[0].ref_panel_median_cov,
-      sample_median_cov: $eqc_outputs[0].bincov_median
+      sample_median_cov: $eqc_outputs[0].bincov_median,
+      "cytobands": $inputs[0].cytobands,
   }' > "${gather_batch_evidence_inputs_json_filename}"
 
 bash /opt/sv_shell/gather_batch_evidence.sh \