separated variants input and add quotes to ensure emptylist works pro…

…perly
ylab-hi · Mar 10, 2024 · 4a01312 · 4a01312
1 parent bbff68e
commit 4a01312
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/workflow/rules/prioritization.smk b/workflow/rules/prioritization.smk
@@ -77,13 +77,13 @@ rule prioritization:
   shell:
     """
       python workflow/scripts/prioritization/compile.py \
-          --SNV {input.snv} \
-          --indels {input.indels} \
-          --long_indels {input.long_indels} \
-          --exitrons {input.exitrons} \
-          --altsplicing {input.altsplicing} \
-          --fusions {input.fusions} \
-          --custom {input.custom} \
+          --SNV "{input.snv}" \
+          --indels "{input.indels}" \
+          --long_indels "{input.long_indels}" \
+          --exitrons "{input.exitrons}" \
+          --altsplicing "{input.altsplicing}" \
+          --fusions "{input.fusions}" \
+          --custom "{input.custom}" \
           --proteome {input.peptide} \
           --anno {input.annotation} \
           --confidence medium \