From a41abb4be5208639cd760aea773a93f67a390ff3 Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Tue, 23 Jan 2024 17:03:25 +0100 Subject: [PATCH] fix: lookup benchmark with correct benchmark name instead of callset name --- workflow/rules/common.smk | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 8df9df7..d4b6f91 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -322,7 +322,8 @@ def get_nonempty_coverages(wildcards): def get_somatic_flag(wildcards): - return '--squash-ploidy' if genomes[benchmarks[wildcards.callset]['genome']]['somatic'] else '' + benchmark = config["variant-calls"][wildcards.callset]["benchmark"] + return '--squash-ploidy' if genomes[benchmarks[benchmark]['genome']]['somatic'] else '' def get_collect_stratifications_input(wildcards):