fix: use proviral_length for proviruses in viral N50/total_bases

ViralOverallSummary was using the full host contig length for provirus
rows, inflating n50_viral and total_viral_bases. Now substitutes
proviral_length (geNomad CheckV, falling back to VirSorter2 CheckV)
when either tool flags a contig as a provirus.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: tpshea2

wdl/tasks/Viral/ViralSummary.wdl

@@ -329,7 +329,18 @@ for row in rows:
     )
     qual_counts[bq] += 1
 
-    cl = row.get('contig_length', '')
+    # Use proviral_length for proviruses so we don't inflate N50/total_bases
+    # with the full host contig. Fall back to vs2 provirus flag if genomad
+    # didn't call it, then fall back to full contig_length if neither flagged it.
+    is_provirus = (
+        row.get('genomad_checkv_provirus', '') == 'Yes' or
+        row.get('vs2_checkv_provirus',     '') == 'Yes'
+    )
+    if is_provirus:
+        cl = (row.get('genomad_checkv_proviral_length', '') or
+              row.get('vs2_checkv_proviral_length',     ''))
+    else:
+        cl = row.get('contig_length', '')
     if cl and cl != 'NA':
         try:
             lengths.append(int(cl))