diff --git a/workflow/rules/neighborhoods.smk b/workflow/rules/neighborhoods.smk index cc5710b35..dce82ec1f 100644 --- a/workflow/rules/neighborhoods.smk +++ b/workflow/rules/neighborhoods.smk @@ -10,7 +10,7 @@ rule create_neighborhoods: genes = lambda wildcards: BIOSAMPLES_CONFIG.loc[wildcards.biosample, 'genes'], ubiquitous_genes = config['ref']['ubiquitous_genes'], chrom_sizes = config['ref']['chrom_sizes'], - qnorm = config['ref']['qnorm'] if config['params_neighborhoods']['use_qnorm'] else None, + qnorm = f"--qnorm {config['ref']['qnorm']}" if config['params_neighborhoods']['use_qnorm'] else "", scripts_dir = SCRIPTS_DIR conda: "../envs/abcenv.yml" @@ -39,6 +39,6 @@ rule create_neighborhoods: --outdir {output.neighborhoodDirectory} \ --genes {output.processed_genes_file} \ --ubiquitously_expressed_genes {params.ubiquitous_genes} \ - --qnorm {params.qnorm} \ - --H3K27ac {params.H3K27ac} + --H3K27ac {params.H3K27ac} \ + {params.qnorm} """ \ No newline at end of file