diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index a94e487..ebf3165 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -89,7 +89,8 @@ def get_bwa_extra(wildcards): Set -q option for independent mapping qualities for split reads (Circle-Map uses this). """ return r"-q -R '@RG\tID:{sample}\tSM:{sample}\tPL:{platform}'".format( - sample=wildcards.sample, platform=samples.loc[wildcards.sample, "platform"] + sample=wildcards.sample, + platform=samples.loc[wildcards.sample, "platform"].upper(), )