diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 933d047..2d72248 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -257,7 +257,7 @@ def get_benchmark_truth(wildcards): def get_stratified_truth(suffix=""): def inner(wildcards): benchmark = config["variant-calls"][wildcards.callset]["benchmark"] - return (f"results/variants/{benchmark}.truth.cov-{{cov}}.vcf.gz{suffix}",) + return (f"results/variants/{benchmark}.truth.cov-{cov}.vcf.gz{suffix}",) return inner @@ -269,7 +269,7 @@ def get_confidence_regions(wildcards): def get_test_regions(wildcards): benchmark = config["variant-calls"][wildcards.callset]["benchmark"] - return f"resources/regions/{benchmark}/test-regions.cov-{{cov}}.bed" + return f"resources/regions/{benchmark}/test-regions.cov-{cov}.bed" def get_rename_contig_file(wildcards): @@ -323,7 +323,9 @@ def get_nonempty_coverages(wildcards): def get_somatic_flag(wildcards): benchmark = config["variant-calls"][wildcards.callset]["benchmark"] return ( - "--squash-ploidy" if genomes[benchmarks[benchmark]["genome"]].get("somatic") else "" + "--squash-ploidy" + if genomes[benchmarks[benchmark]["genome"]].get("somatic") + else "" )