From 8640c2260ab353c1c73e2222476ad53ab6fa213b Mon Sep 17 00:00:00 2001
From: magdalenazz <magdalenazz477@gmail.com>
Date: Mon, 22 Jul 2024 14:04:24 +0200
Subject: [PATCH] bug: linting

---
 docs/softwares.md                  | 4 ++++
 workflow/rules/happy.smk           | 3 ++-
 workflow/schemas/rules.schema.yaml | 8 ++++----
 3 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/docs/softwares.md b/docs/softwares.md
index 47b7b72..9d133fc 100644
--- a/docs/softwares.md
+++ b/docs/softwares.md
@@ -78,6 +78,10 @@ To compare a VCF against a gold standard dataset.
 
 #### :left_right_arrow: input / output files
 
+print(f"rule_schema: {rule_schema}")
+print(f"section_key: {section_key}")
+print(f"variable_key: {variable_key}")
+
 #SNAKEMAKE_RULE_TABLE__happy__happy#
 
 ### :wrench: Configuration
diff --git a/workflow/rules/happy.smk b/workflow/rules/happy.smk
index bcfa6d8..2279712 100644
--- a/workflow/rules/happy.smk
+++ b/workflow/rules/happy.smk
@@ -27,7 +27,8 @@ rule happy:
             ".roc.Locations.INDEL.PASS.csv.gz",
             ".roc.Locations.SNP.csv.gz",
             ".roc.tsv",
-        ),
+        ),        
+        dummy="qc/happy/{sample}_{type}.vcf.gz",
     params:
         engine="vcfeval",
         prefix=lambda wc, input, output: output[0].split(".")[0],
diff --git a/workflow/schemas/rules.schema.yaml b/workflow/schemas/rules.schema.yaml
index 3e690eb..f1d2b2f 100644
--- a/workflow/schemas/rules.schema.yaml
+++ b/workflow/schemas/rules.schema.yaml
@@ -74,7 +74,6 @@ properties:
             type: string
             description: Pileup file with allele information for selected sites
 
-  # Entry added using Hydra-Genetics CLI - please move it into alphabetically sorted order
   happy:
     type: object
     description: input and output parameters for happy
@@ -106,10 +105,11 @@ properties:
             description: directory for stratifications   
       output:
         type: object
-        description: list of outputs
+        description: list of inputs
         properties:
-          type: string
-          description: list of a range of outputfiles produced
+          dummy:
+            type: string
+            description: VCF file
 
   longqc_sampleqc:
     type: object