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genomic-medicine-sweden · Sep 22, 2023 · 8941562 · 8941562
1 parent 4816f45
commit 8941562
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/requirements.test.txt b/requirements.test.txt
@@ -1,4 +1,4 @@
 networkx==2.7
 pycodestyle==2.8.0
 pytest==6.2.5
-snakefmt==0.6.0
+snakefmt==0.8.4
diff --git a/workflow/Snakefile_references.smk b/workflow/Snakefile_references.smk
@@ -18,10 +18,11 @@ rule all:
 # purecn will be fetching normaldb and intervals from the config
 # and we want to use the newly generated files. There fore we overide
 # the config point to files created by references pipeline.
+# ToDo override rules instead
 config["purecn"]["normaldb"] = "references/purecn_normal_db/output/normalDB_hg19.rds"
 config["purecn"]["intervals"] = "references/purecn_interval_file/targets_intervals.txt"
-config['reference']['design_intervals'] = "references/preprocess_intervals/design.preprocessed.interval_list"
-config['reference']['design_intervals_gatk_cnv'] = "references/preprocess_intervals/design.preprocessed.interval_list"
+config["reference"]["design_intervals"] = "references/preprocess_intervals/design.preprocessed.interval_list"
+config["reference"]["design_intervals_gatk_cnv"] = "references/preprocess_intervals/design.preprocessed.interval_list"
 
 
 module pipeline: