diff --git a/src/salmon.snake b/src/salmon.snake index 867e397..553c769 100644 --- a/src/salmon.snake +++ b/src/salmon.snake @@ -37,7 +37,8 @@ rule salmon_quant_se: r1 = salmon_input_r1, index = rules.salmon_index.output output: - config['dirs']['quant'] + '/{sample}/quant.sf' + config['dirs']['quant'] + '/{sample}/quant.sf', + config['dirs']['quant'] + '/{sample}/aux_info/meta_info.json' params: flags = config['salmon']['quant_flags'] if 'quant_flags' in config.get('salmon', {}) else '' log: @@ -72,7 +73,7 @@ rule salmon_stats: column_values = [find_nested_key(data, k.split(':')) for k in params.columns] keep_column = [not x for x in map(lambda x: x is None or isinstance(x, dict), column_values)] - + sample_row = dict(zip([params.columns[i] for i in range(len(params.columns)) if keep_column[i]], [column_values[i] for i in range(len(column_values)) if keep_column[i]])) stats.append(sample_row)