Remove vcf dir

PMBio · Dec 5, 2023 · 50d1d6b · 50d1d6b
1 parent 382489a
commit 50d1d6b
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Showing 2 changed files with 1 addition and 3 deletions.
diff --git a/pipelines/config/deeprvat_preprocess_config.yaml b/pipelines/config/deeprvat_preprocess_config.yaml
@@ -11,7 +11,6 @@ working_dir: workdir
 data_dir: data
 
 # These paths are all relative to the data dir
-input_vcf_dir_name : vcf
 metadata_dir_name: metadata
 
 # These paths are all relative to the working dir
@@ -34,4 +33,4 @@ vcf_files_list: vcf_files_list.txt
 preprocess_threads: 16
 
 # You can specify a different zcat cmd for example gzcat here, default zcat
-zcat_cmd:
+zcat_cmd: gzcat
diff --git a/pipelines/preprocess.snakefile b/pipelines/preprocess.snakefile
@@ -12,7 +12,6 @@ preprocessing_cmd = "deeprvat_preprocess"
 working_dir = Path(config["working_dir"])
 data_dir = Path(config["data_dir"])
 preprocessed_dir = working_dir / config["preprocessed_dir_name"]
-vcf_dir = data_dir / config["input_vcf_dir_name"]
 metadata_dir = data_dir / config["metadata_dir_name"]
 reference_dir = working_dir / config["reference_dir_name"]