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common.smk: allow for lowercase platform specification in samples.tsv
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this should allow for easier compatibility with samples.tsv files for the cyrcular-calling workflow
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dlaehnemann authored Jan 11, 2024
1 parent 6f450f0 commit e57839f
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion workflow/rules/common.smk
Original file line number Diff line number Diff line change
Expand Up @@ -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()
)


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