Write index output to log file
Writes output from the augur index command to the rule's log file (which
was defined in the rule but unused).
Related to
@@ -347,7 +347,7 @@ rule index_sequences:
"""
augur index \
--sequences {input.sequences} \
- --output {output.sequence_index}
+ --output {output.sequence_index} 2>&1 | tee {log}
"""
rule subsample:
