Merge branch 'master' into feat/varpubs

Author: FelixMoelder

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [6.6.1](https://github.com/snakemake-workflows/dna-seq-varlociraptor/compare/v6.6.0...v6.6.1) (2026-03-18)
+
+
+### Miscellaneous Chores
+
+* release 6.6.1 ([4ecaa79](https://github.com/snakemake-workflows/dna-seq-varlociraptor/commit/4ecaa7939bf3e555dac12cea6fed7d7e605a7b38))
+
 ## [6.6.0](https://github.com/snakemake-workflows/dna-seq-varlociraptor/compare/v6.5.2...v6.6.0) (2026-03-06)
 
 

workflow/rules/candidate_calling.smk

@@ -18,7 +18,7 @@ rule freebayes:
             config["params"]["freebayes"].get("min_alternate_fraction", "0.05"),
             config["params"]["freebayes"].get("extra", ""),
         ),
-    threads: max(workflow.cores - 1, 1)  # use all available cores -1 (because of the pipe) for calling
+    threads: 96  # with more cores, we expect freebayes to become too IO bound and memory hungry
     wrapper:
         "v2.7.0/bio/freebayes"
 

workflow/rules/table.smk

@@ -11,7 +11,7 @@ rule vembrane_table:
     log:
         "logs/vembrane-table/{group}.{event}.{calling_type}.log",
     shell:
-        'vembrane table --header "{params.config[header]}" "{params.config[expr]}" '
+        'vembrane table --wide --header "{params.config[header]}" "{params.config[expr]}" '
         "{input.bcf} > {output.bcf} 2> {log}"
 
 

workflow/schemas/config.schema.yaml

@@ -1,4 +1,4 @@
-$schema: "http://json-schema.org/draft-07/schema#"
+$schema: "https://json-schema.org/draft/2020-12/schema"
 
 description: snakemake configuration file
 
@@ -31,7 +31,7 @@ definitions:
     properties:
       varlociraptor:
         type: array
-        items: 
+        items:
           type: string
       filter:
         anyOf:
@@ -93,7 +93,7 @@ properties:
       trimming:
         type: object
         properties:
-          activate: 
+          activate:
             type: boolean
           primers_fq1:
             type: string
@@ -145,7 +145,7 @@ properties:
             type: string
           events:
             type: array
-            items: 
+            items:
               type: string
         required:
           - activate
@@ -164,7 +164,7 @@ properties:
             type: boolean
           annotation_fields:
             type: array
-            items: 
+            items:
                anyOf:
                 - type: string
                 - type: object
@@ -224,7 +224,7 @@ properties:
             type: boolean
           mode:
             type: string
-            enum: 
+            enum:
               - local-smart
               - local-strict
               - global-smart
@@ -240,7 +240,7 @@ properties:
       - scenario
       - filter
       - fdr-control
-  
+
   remove_duplicates:
     type: object
     properties:
@@ -266,7 +266,7 @@ properties:
             type: boolean
           datasources:
             type: array
-            items: 
+            items:
               type: string
       vep:
         properties:

workflow/schemas/primers.schema.yaml

@@ -1,4 +1,4 @@
-$schema: "http://json-schema.org/draft-04/schema#"
+$schema: "https://json-schema.org/draft/2020-12/schema"
 description: row of the primer_panels.tsv, representing a primer panel, i.e. single-end or paired-end data
 type: object
 properties:

workflow/schemas/samples.schema.yaml

@@ -65,4 +65,4 @@ required:
   - calling
 
 dependentRequired:
-  umi_read: ["umi_len"]
+  umi_read: ["umi_len"]

workflow/schemas/units.schema.yaml

@@ -1,4 +1,4 @@
-$schema: "http://json-schema.org/draft-04/schema#"
+$schema: "https://json-schema.org/draft/2020-12/schema"
 description: row of the units.tsv, representing a sequencing unit, i.e. single-end or paired-end data
 type: object
 properties: