From e3702fac1127bd60c046425d6283b57aa57ece6e Mon Sep 17 00:00:00 2001
From: magdalenazz <magdalenazz477@gmail.com>
Date: Wed, 17 Jul 2024 16:37:54 +0200
Subject: [PATCH] bug: Linting init

---
 .tests/integration/config.yaml     |  4 ++++
 workflow/rules/happy.smk           | 32 ++++++++++++++++++++----------
 workflow/schemas/rules.schema.yaml |  4 ++--
 3 files changed, 27 insertions(+), 13 deletions(-)

diff --git a/.tests/integration/config.yaml b/.tests/integration/config.yaml
index 1b02918..b794997 100644
--- a/.tests/integration/config.yaml
+++ b/.tests/integration/config.yaml
@@ -21,6 +21,10 @@ gatk_get_pileup_summaries:
   sites: "reference/chr1_small_exac_common_3.hg19.vcf"
   variants: "reference/chr1_small_exac_common_3.hg19.vcf"
 
+happy:
+  container: "docker://hydragenetics/hap.py:0.3.15"
+  extra: ""
+
 mosdepth:
   by: "500"
   container: "docker://hydragenetics/mosdepth:0.3.2"
diff --git a/workflow/rules/happy.smk b/workflow/rules/happy.smk
index 76dfd28..bcfa6d8 100644
--- a/workflow/rules/happy.smk
+++ b/workflow/rules/happy.smk
@@ -14,21 +14,31 @@ rule happy:
         genome=config.get("reference", {}).get("fasta", ""),
         genome_index=config.get("reference", {}).get("fai", ""),
     output:
-        multiext("qc/happy/{sample}_{type}.","results",".runinfo.json",".vcf.gz",".summary.csv",
-                ".extended.csv",".metrics.json.gz",".roc.all.csv.gz",
-                ".roc.Locations.INDEL.csv.gz",".roc.Locations.INDEL.PASS.csv.gz",
-                ".roc.Locations.SNP.csv.gz",".roc.tsv")
+        multiext(
+            "qc/happy/{sample}_{type}.",
+            "results",
+            ".runinfo.json",
+            ".vcf.gz",
+            ".summary.csv",
+            ".extended.csv",
+            ".metrics.json.gz",
+            ".roc.all.csv.gz",
+            ".roc.Locations.INDEL.csv.gz",
+            ".roc.Locations.INDEL.PASS.csv.gz",
+            ".roc.Locations.SNP.csv.gz",
+            ".roc.tsv",
+        ),
     params:
         engine="vcfeval",
-        prefix=lambda wc, input, output: output[0].split('.')[0],
+        prefix=lambda wc, input, output: output[0].split(".")[0],
         ## parameters such as -L to left-align variants
-        extra="--verbose"
-    log: "qc/happy/{sample}_{type}.happy.log"
-        container:
+        extra="--verbose",
+    log:
+        "qc/happy/{sample}_{type}.happy.log",
+    container:
         config.get("happy", {}).get("container", config["default_container"])
     message:
         "{rule}: Happy is for benchmarking variant accuracy of {input.query} compared to {input.truth}"
     threads: config.get("happy", {}).get("threads", config["default_resources"]["threads"])
-    wrapper: "v3.13.7/bio/hap.py/hap.py"
-
-
+    wrapper:
+        "v3.13.7/bio/hap.py/hap.py"
diff --git a/workflow/schemas/rules.schema.yaml b/workflow/schemas/rules.schema.yaml
index 8dff26f..a9d951d 100644
--- a/workflow/schemas/rules.schema.yaml
+++ b/workflow/schemas/rules.schema.yaml
@@ -101,9 +101,9 @@ properties:
           strats:
             type: string
             description: stratifications.tsv reference file
-           strats:
+           strat_dir:
             type: string
-            description: directory    
+            description: directory for stratifications   
       output:
         type: object
         description: list of outputs