I'm wondering how Snakemake deals with output to stdout
and stderr
that is generated when running a rule with a shell:
command.
I ran the following rule and only got informed that there was a non-zero exit code. However, I did not get a stack trace. To get access to the stack trace I had to run the shell command manually:
# Shortened for clarity
rule parse:
input:
sequences = rules.join_downloads.output
output:
sequences = "data/sequences.fasta"
shell:
"""
augur parse
"""
Why is that? And can I somehow make Snakemake output more detailed information when something goes wrong to help with debugging?