I trying to run a snakemake workflow. What I want to do is that if a given rule (rule a) works out send an email with a small text saying so, and if it fails then send another different email indicating an ERROR. I was wondering, is there a way in snakemake to run something similar to a try-except python block?
I have already tried out the try-except block with some commands inside a shell() directive, but it seems that I am not allowed to run any python code (except part of the block) once I have already written a shell() directive.
I think your options are to convert your shell directive into a run directive with shell() functions or to use bash. For bash, something like
shell:
'MyCommandThatMayFail '
'&& mail -s "passed" [email protected] '
'|| (mail -s "failed" [email protected] ; exit 1)'
Should work for the email. The exit 1 is necessary to signal to snakemake that the command failed.
A final consideration, if you are using a job scheduler on a cluster, the worker nodes may not have network access so emailing will fail from the submitted jobs.