snakefmt

PMBio · Dec 5, 2023 · b5ac677 · b5ac677
1 parent 2e1deec
commit b5ac677
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/pipelines/preprocess_no_qc.snakefile b/pipelines/preprocess_no_qc.snakefile
@@ -1,11 +1,13 @@
 include: "preprocessing/preprocess.snakefile"
 
+
 rule all:
     input:
         preprocessed_dir / "genotypes.h5",
         norm_variants_dir / "variants.tsv.gz",
         variants=norm_variants_dir / "variants.parquet",
 
+
 rule preprocess_no_qc:
     input:
         variants=norm_variants_dir / "variants.tsv.gz",

diff --git a/pipelines/preprocessing/preprocess.snakefile b/pipelines/preprocessing/preprocess.snakefile
@@ -1,7 +1,9 @@
 from pathlib import Path
 
+
 configfile: "config/deeprvat_preprocess_config.yaml"
 
+
 load_samtools = config.get("samtools_load_cmd") or ""
 load_bcftools = config.get("bcftools_load_cmd") or ""
 zcat_cmd = config.get("zcat_cmd") or "zcat"
@@ -37,9 +39,8 @@ qc_filtered_samples_dir = qc_dir / "filtered_samples"
 
 
 with open(config["vcf_files_list"]) as file:
-
     vcf_files = [Path(line.rstrip()) for line in file]
-    vcf_stems = [vf.stem.replace(".vcf","") for vf in vcf_files]
+    vcf_stems = [vf.stem.replace(".vcf", "") for vf in vcf_files]
 
     assert len(vcf_stems) == len(vcf_files)