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remove issues with snakemake and {{ escaping in format strings
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Nicolai-vKuegelgen committed Jul 30, 2024
1 parent 28414bf commit 1fe8fdb
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions stemcnv_check/rules/StemCNV-check.smk
Original file line number Diff line number Diff line change
Expand Up @@ -104,9 +104,9 @@ def fix_container_path(path_in, bound_to):
def get_cnv_vcf_output(mode):
addition = config['settings']['make_cnv_vcf']['name_addition']
if mode == 'combined-calls':
return os.path.join(DATAPATH, "{sample_id}", f"{{sample_id}}.combined-cnv-calls{addition}.vcf")
return os.path.join(DATAPATH, "{sample_id}", "{{sample_id}}.combined-cnv-calls{0}.vcf".format(addition))
elif mode == 'split-tools':
return [os.path.join(DATAPATH, "{sample_id}", f"{{sample_id}}.{tool}-cnv-calls{addition}.vcf")
return [os.path.join(DATAPATH, "{sample_id}", "{{sample_id}}.{tool}-cnv-calls{0}.vcf".format(addition))
for tool in config['settings']['CNV.calling.tools']]
else:
raise ConfigValueError('Value not allowed for settings$make.cnv.vcf$mode: "{}"'.format(config['settings']['make_cnv_vcf']['mode']))
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