From e57839f1737fafd484b0b5edf3d319a009bd08a3 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Thu, 11 Jan 2024 12:52:37 +0100 Subject: [PATCH] common.smk: allow for lowercase platform specification in samples.tsv this should allow for easier compatibility with samples.tsv files for the cyrcular-calling workflow --- workflow/rules/common.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index a94e487..90b8732 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -89,7 +89,7 @@ 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() )