fix: added option to skip pangenome analysis

Author: m-jahn

.test/config/config.yml

@@ -23,6 +23,7 @@ quast:
   extra: ""
 
 panaroo:
+  skip: False
   remove_source: "cmsearch"
   remove_feature: "tRNA|rRNA|ncRNA|exon|sequence_feature"
   extra: "--clean-mode strict --remove-invalid-genes"

config/config.yml

@@ -23,6 +23,7 @@ quast:
   extra: ""
 
 panaroo:
+  skip: False
   remove_source: "cmsearch"
   remove_feature: "tRNA|rRNA|ncRNA|exon|sequence_feature"
   extra: "--clean-mode strict --remove-invalid-genes"

config/schemas/config.schema.yml

@@ -83,6 +83,9 @@ properties:
   panaroo:
     type: object
     properties:
+      skip:
+        type: boolean
+        description: Whether to skip Panaroo analysis
       remove_source:
         type: string
         description: Source types to remove in Panaroo (regex supported)

workflow/rules/common.smk

@@ -58,7 +58,7 @@ def get_final_input(wildcards):
         "results/qc/quast/{tool}/report.txt",
         tool=config["tool"],
     )
-    if len(samples.index) > 1:
+    if len(samples.index) > 1 and not config["panaroo"]["skip"]:
         inputs += expand(
             "results/qc/panaroo/{tool}/summary_statistics.txt",
             tool=config["tool"],