I'm wondering how Snakemake deals with output to
stderr that is generated when running a rule with a
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?