diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index ec08d00..1dc6a6b 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -104,7 +104,7 @@ def get_plot_cov_labels(): # TODO check if ever used anywhere def get_truth_url(wildcards, input): genome = genomes[wildcards.genome] - truth = genome["truth"][get_genome_build(wildcards)] + truth = genome["truth"][get_genome_build()] if isinstance(truth, dict): truth = truth[wildcards.truthset] if input.archive: @@ -116,7 +116,7 @@ def get_truth_url(wildcards, input): def get_truthsets(csi=False): def inner(wildcards): genome = genomes[wildcards.genome] - truthsets = genome["truth"][get_genome_build(wildcards)] + truthsets = genome["truth"][get_genome_build()] if csi: return expand( "resources/variants/{genome}/{truthset}.truth.bcf.csi", @@ -147,8 +147,11 @@ def get_confidence_bed_cmd(wildcards, input): return f"curl --insecure -L {bed} {unpack_cmd}" -def get_genome_build(wildcards): - return config["variant-calls"][wildcards.callset]["genome-build"] +def get_genome_build(): + if config.get("grch37"): + return "grch37" + else: + return "grch38" def get_io_prefix(getter):