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Bugfix: Salmon meta info output
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jenzopr committed Jun 18, 2018
1 parent d5d77b7 commit f08b04d
Showing 1 changed file with 3 additions and 2 deletions.
5 changes: 3 additions & 2 deletions src/salmon.snake
Original file line number Diff line number Diff line change
@@ -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)

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