fix: multiple minor fixes

FelixMoelder · FelixMoelder · commit 7472d1c648f5 · 2025-07-04T10:59:51.000+02:00
diff --git a/workflow/envs/arriba.post-deploy.sh b/workflow/envs/arriba.post-deploy.sh
diff --git a/workflow/envs/arriba.yaml b/workflow/envs/arriba.yaml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - arriba =2.4
+  - arriba =2.5
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -11,7 +11,7 @@ samples = (
     pd.read_csv(
         config["samples"],
         sep="\t",
-        dtype={"sample_name": str, "group": str},
+        dtype={"sample_name": str, "group": str, "umi_len": "Int64"},
         comment="#",
     )
     .set_index("sample_name", drop=False)
diff --git a/workflow/rules/fusion_calling.smk b/workflow/rules/fusion_calling.smk
@@ -1,6 +1,6 @@
 module fusion_calling:
     meta_wrapper:
-        "v3.13.3/meta/bio/star_arriba"
+        "v7.1.0/meta/bio/star_arriba"
     config:
         config
 
diff --git a/workflow/scripts/split-call-tables.py b/workflow/scripts/split-call-tables.py
@@ -173,7 +173,6 @@ def variants(
             self.pos = pos
             self._variants = self._load_variants()
         for variant in self._variants:
-            print(variant.pos)
             if variant.pos == pos and variant.alts[0] == alt:
                 yield variant
             if variant.pos > pos:

Original file line number	Diff line number	Diff line change
`@@ -11,7 +11,7 @@ samples = (`
`11`	`11`	`pd.read_csv(`
`12`	`12`	`config["samples"],`
`13`	`13`	`sep="\t",`
`14`		`- dtype={"sample_name": str, "group": str},`
	`14`	`+ dtype={"sample_name": str, "group": str, "umi_len": "Int64"},`
`15`	`15`	`comment="#",`
`16`	`16`	`)`
`17`	`17`	`.set_index("sample_name", drop=False)`