bug: linting

hydra-genetics · Jul 23, 2024 · 93ced62 · 93ced62
1 parent 26fb70f
commit 93ced62
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Showing 3 changed files with 6 additions and 10 deletions.
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -79,7 +79,7 @@ def compile_output_list(wildcards):
         "qc/peddy/peddy.peddy.ped",
         "qc/peddy/peddy.ped_check.csv",
         "qc/peddy/peddy.sex_check.csv",
-        "qc/peddy/peddy.het_check.csv",zx
+        "qc/peddy/peddy.het_check.csv",
         "qc/peddy/peddy.html",
         "qc/peddy/peddy.vs.html",
         "qc/peddy/peddy.background_pca.json",

diff --git a/workflow/rules/happy.smk b/workflow/rules/happy.smk
@@ -6,11 +6,10 @@ __license__ = "GPL-3"
 
 rule happy:
     input:
-        truth="truth.vcf",
-        query="parabricks/pbrun_deepvariant/{sample}_{type}.vcf.gz",
-        truth_regions="truth.bed",
-        strats="stratifications.tsv",
-        strat_dir="strats_dir",
+        truth="reference/happy.truth.vcf",
+        query="reference/happy.test.vcf",
+        truth_regions="reference/happy.bed",
+        strats="stratifications.tsv", # optional, from https://github.com/genome-in-a-bottle/genome-stratifications
         genome=config.get("reference", {}).get("fasta", ""),
         genome_index=config.get("reference", {}).get("fai", ""),
     output:

diff --git a/workflow/schemas/rules.schema.yaml b/workflow/schemas/rules.schema.yaml
@@ -99,10 +99,7 @@ properties:
             description: BED reference file for which regions should be evaluated
           strats:
             type: string
-            description: stratifications.tsv reference file
-          strat_dir:
-            type: string
-            description: directory for stratifications   
+            description: stratifications.tsv reference file, optional from https://github.com/genome-in-a-bottle/genome-stratifications
       output:
         type: object
         description: list of inputs