script: fix cli --clades arg parsing for scr2rf.sh

ktmeaton · Oct 3, 2022 · 9300772 · 9300772
1 parent bed29fd
commit 9300772
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Showing 2 changed files with 7 additions and 6 deletions.
diff --git a/scripts/sc2rf.sh b/scripts/sc2rf.sh
@@ -12,11 +12,6 @@ while [[ $# -gt 0 ]]; do
       shift # past argument
       shift # past value
       ;;
-    --clades)
-      clades=$2
-      shift # past argument
-      shift # past value
-      ;;
     --primers)
       primers=$2
       shift # past argument
@@ -57,6 +52,12 @@ while [[ $# -gt 0 ]]; do
         shift # past value
       fi
       ;;
+    *)
+      # This is a risky way to parse the clades for sc2rf
+      value=$1
+      sc2rf_args+=("$value")
+      shift # past value
+      ;;
   esac
 done
 

diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -480,7 +480,7 @@ rule sc2rf:
     "logs/{rule}/{{build}}_{{mode}}_{today}.log".format(today=today, rule=rule_name),
   shell:
     """
-    bash scripts/sc2rf.sh \
+    scripts/sc2rf.sh \
       --alignment {input.alignment} \
       --output-ansi {output.ansi} \
       --output-csv {output.csv} \