fix: activate report creation in test case and fix remaining problems

Author: dlaehnemann

.test/config-sra/config.yaml

@@ -132,7 +132,7 @@ gene_coverage:
   min_avg_coverage: 8
 
 report:
-  activate: false
+  activate: true
   max_read_depth: 250
   stratify:
     activate: false

workflow/rules/common.smk

@@ -1526,7 +1526,7 @@ def get_datavzrd_data(impact="coding"):
         return expand(
             pattern,
             impact=impact,
-            event=wildcards.any_event,
+            any_event=wildcards.any_event,
             group=get_report_batch(calling_type),
         )
 

workflow/rules/table.smk

@@ -1,15 +1,15 @@
 rule vembrane_table:
     input:
-        bcf="results/final-calls/{group}.{event}.{calling_type}.fdr-controlled.normal-probs.bcf",
+        bcf="results/final-calls/{group}.{any_event}.{calling_type}.fdr-controlled.normal-probs.bcf",
         scenario="results/scenarios/{group}.yaml",
     output:
-        bcf="results/tables/{group}.{event}.{calling_type}.fdr-controlled.tsv",
+        bcf="results/tables/{group}.{any_event}.{calling_type}.fdr-controlled.tsv",
     conda:
         "../envs/vembrane.yaml"
     params:
         config=lambda wc, input: get_vembrane_config(wc, input),
     log:
-        "logs/vembrane-table/{group}.{event}.{calling_type}.log",
+        "logs/vembrane-table/{group}.{any_event}.{calling_type}.log",
     shell:
         'vembrane table --header "{params.config[header]}" "{params.config[expr]}" '
         "{input.bcf} > {output.bcf} 2> {log}"