Fix Genomad task: handle absent virus FASTA when no viral sequences found

geNomad skips writing the virus .fna when it finds no viral sequences, causing
the hardcoded cp to fail. Switch to find-based glob so the output path is also
robust to geNomad prefix naming variations (.fasta.gz stripping behavior).

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

Author: tpshea2

wdl/tasks/Viral/Genomad.wdl

@@ -78,11 +78,24 @@ task Genomad {
             genomad_out \
             "${DB_PATH}"
 
-        # Rename outputs with sample prefix
-        cp genomad_out/input_contigs_summary/input_contigs_virus_summary.tsv \
-           ~{sample_name}.genomad_virus_summary.tsv
-        cp genomad_out/input_contigs_virus/input_contigs_virus.fna \
-           ~{sample_name}.genomad_virus.fna
+        # Rename outputs with sample prefix.
+        # The virus FASTA is absent when geNomad finds no viral sequences; touch an
+        # empty file so WDL output declaration is always satisfied.
+        SUMMARY_TSV=$(find genomad_out -name '*_virus_summary.tsv' 2>/dev/null | head -1)
+        if [[ -n "${SUMMARY_TSV}" ]]; then
+            cp "${SUMMARY_TSV}" ~{sample_name}.genomad_virus_summary.tsv
+        else
+            touch ~{sample_name}.genomad_virus_summary.tsv
+            echo "WARNING: geNomad produced no virus_summary.tsv — no viral sequences found" >&2
+        fi
+
+        VIRUS_FNA=$(find genomad_out -name '*_virus.fna' 2>/dev/null | head -1)
+        if [[ -n "${VIRUS_FNA}" ]]; then
+            cp "${VIRUS_FNA}" ~{sample_name}.genomad_virus.fna
+        else
+            touch ~{sample_name}.genomad_virus.fna
+            echo "WARNING: geNomad produced no virus.fna — no viral sequences found" >&2
+        fi
     >>>
 
     output {