diff --git a/buisciii/templates/viralrecon/ANALYSIS/lablog_viralrecon b/buisciii/templates/viralrecon/ANALYSIS/lablog_viralrecon index 5aae8c10..50e12a2c 100644 --- a/buisciii/templates/viralrecon/ANALYSIS/lablog_viralrecon +++ b/buisciii/templates/viralrecon/ANALYSIS/lablog_viralrecon @@ -63,25 +63,28 @@ while getopts "MAmapsrfh" opt; do fi ;; p) - if [[ -n $virus_tag || $monkeypox == "y" ]]; then + if [[ $selected_virus == "yes" ]]; then echo "Error: options -p, -s, and -r cannot be selected simultaneously." exit 1 fi monkeypox="y" # Monkeypox virus + selected_virus="yes" ;; s) - if [[ -n $virus_tag || $monkeypox == "y" ]]; then + if [[ $selected_virus == "yes" ]]; then echo "Error: options -p, -s, and -r cannot be selected simultaneously." exit 1 fi virus_tag="sars-cov-2" # SARS-CoV-2 + selected_virus="yes" ;; r) - if [[ -n $virus_tag || $monkeypox == "y" ]]; then + if [[ $selected_virus == "yes" ]]; then echo "Error: options -p, -s, and -r cannot be selected simultaneously." exit 1 fi virus_tag="rsv" # RSV + selected_virus="yes" ;; f) samples_ref_prepared="y"