Log executed shell command from snakemake - snakemake

Question

I'd like to save the shell command executed by each snakemake job to a log file.
With --printshellcmds I can print to stdout the shell commands as they are submitted but I would like to save them to individual files. For example, this script:
samples= ['a', 'b', 'c']
rule all:
input:
expand('{sample}.done', sample= samples),
rule do_stuff:
output:
'{sample}.done'
shell:
"""
echo {wildcards.sample} > {output}
"""
will execute the 3 jobs:
echo a > a.done
echo c > c.done
echo b > b.done
I'd like to save each of these to a separate file named after a wildcard (or whatever). Like:
rule do_stuff:
output:
'{sample}.done'
log_shell: < save shell command
'{sample}.cmd.log' <
shell:
"""
echo {wildcards.sample} > {output}
"""
Is this possible? Thank you!

Answer 1

While fiddling with other issues, I came up with this solution. Combine the rundirective with the shell function to first write the command to file and then execute the command itself. Example:
rule do_stuff:
output:
'{sample}.done'
log:
cmd= 'my/logs/{sample}.log'
run:
cmd= """
echo hello > {output}
"""
shell("sort --version > {log.cmd} || true") # Log version
shell("cat <<'EOF' >> {log.cmd}" + cmd) # Log command
shell(cmd) # Exec command
For each {sample} you get a file my/logs/{sample}.log that looks like this:
sort (GNU coreutils) 5.93
Copyright (C) 2005 Free Software Foundation, Inc.
echo hello > a.done
This does the trick. However, it makes the code more cluttered and you effectively lose the --printshellcmds option.