diff --git a/Snakefile b/Snakefile index 44bf7b5b7fcfa0d1fb545b3c19fd358456c96d15..9876c7270bea945765a191363799899409f36790 100644 --- a/Snakefile +++ b/Snakefile @@ -963,10 +963,10 @@ rule prepare_files_for_report: sample=[i for i in list(samples_table.index.values)], seqmode=[samples_table.loc[i, 'seqmode'] for i in list(samples_table.index.values)]), - alfa_concat_out = expand(os.path.join( + alfa_concat_out = os.path.join( config["output_dir"], "ALFA", - "ALFA_plots.concat.png")) + "ALFA_plots.concat.png") output: samples_dir = directory(os.path.join( @@ -1165,6 +1165,14 @@ rule prepare_files_for_report: params.results_dir, "TIN scores_mqc.pdf")) + # adjust alfa plot filename for MutliQC recognition + os.rename( + input.alfa_concat_out, + os.path.join( + params.results_dir, + "ALFA", + "ALFA_plots.concat_mqc.png")) + rule prepare_MultiQC_config: ''' @@ -1223,6 +1231,10 @@ rule prepare_MultiQC_config: YAML.write(" path_filters:\n") YAML.write(" - \"*/map_genome/*\"\n") YAML.write("\n") + YAML.write(" - alfa:\n") + YAML.write(" path_filters:\n") + YAML.write(" - \"*/ALFA_plots.concat_mqc.png\"\n") + YAML.write("\n") YAML.write(" - TIN_scores:\n") YAML.write(" path_filters:\n") YAML.write(" - \"*/TIN scores_mqc.png\"\n")