I am using snakemake to build a workflow. I want that stderr and stdout of all rules are by default redirected into files logs/{rule}/{wildcards}.o and logs/{rule}/{wildcards}.e, respectively. How can I achieve this?
The following code does what I want by prepending to the shell command of a given rule. However, I do not want to add this to each rule. I tried to use shell.prefix(...), which prefixes commands to each rule, but I cannot find a way to access the rule name or the rule wildcards there.
SAMPLES = ['A', 'B']
rule all:
input:
expand('test.{sample}',sample=SAMPLES)
rule test_rule:
output: 'test.{sample}'
shell:
#These three lines need to be prepended for logging.
'mkdir -p logs/{rule}; '
'exec 2> logs/{rule}/{wildcards}.e; '
'exec 1> logs/{rule}/{wildcards}.o; '
#This is the actual code for the rule
'touch {output}; '
'echo "test for {wildcards.sample} created";'
' >&2 echo "error message"'
The above code gives the expected result of log files with stdout and stderr in logs/{rule}/{wildcards}.o/e, but I want to set this globally and not for each rule.
