From 7851f5979c37286edc6293af0853f54d3f00528c Mon Sep 17 00:00:00 2001
From: whalleyt <whalleyt@cardiff.ac.uk>
Date: Wed, 10 Jan 2024 11:18:17 +0000
Subject: [PATCH] remove reference to gnomonicus

---
 modules/clockworkModules.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/clockworkModules.nf b/modules/clockworkModules.nf
index 4a2675d..d793a34 100644
--- a/modules/clockworkModules.nf
+++ b/modules/clockworkModules.nf
@@ -206,7 +206,7 @@ process callVarsCortex {
 
 process minos {
     /**
-    * @QCcheckpoint check if top species is TB, if yes pass vcf to gnomonicus
+    * @QCcheckpoint check if top species is TB, if yes pass vcf to resistance profiling
     */
 
     tag { sample_name }
@@ -241,7 +241,7 @@ process minos {
 
     cp ${sample_name}_report.json ${sample_name}_report_previous.json
 
-    if [[ \$top_hit =~ ^"Mycobacterium tuberculosis" ]]; then printf "CREATE_ANTIBIOGRAM_${sample_name}"; else echo '{"gnomonicus-warning":"sample is not TB so cannot produce antibiogram using gnomonicus"}' | jq '.' > ${error_log} && printf "no" && jq -s ".[0] * .[1]" ${error_log} ${sample_name}_report_previous.json > ${report_json}; fi
+    if [[ \$top_hit =~ ^"Mycobacterium tuberculosis" ]]; then printf "CREATE_ANTIBIOGRAM_${sample_name}"; else echo '{"resistance-profiling-warning":"sample is not TB so cannot produce antibiogram using resistance profiling tools"}' | jq '.' > ${error_log} && printf "no" && jq -s ".[0] * .[1]" ${error_log} ${sample_name}_report_previous.json > ${report_json}; fi
     """
 
     stub:
@@ -296,7 +296,7 @@ process gvcf {
 
     cp ${sample_name}_report.json ${sample_name}_report_previous.json
 
-    if [ ${params.vcfmix} == "no" ] && [ ${params.gnomonicus} == "no" ]; then echo '{"complete":"workflow complete without error"}' | jq '.' > ${error_log} && jq -s ".[0] * .[1]" ${error_log} ${sample_name}_report_previous.json > ${report_json}; fi
+    if [ ${params.vcfmix} == "no" ] && [ ${params.resistance_profiler} == "none" ]; then echo '{"complete":"workflow complete without error"}' | jq '.' > ${error_log} && jq -s ".[0] * .[1]" ${error_log} ${sample_name}_report_previous.json > ${report_json}; fi
     """
 
     stub: