Snakemake+Tibanna should upload log files

[nhartwic]

When using tibanna as a back end for snakemake, it would be nice if log output would be uploaded regardless of if the job fails. This would make debugging a lot easier. As is, getting files back from a failed run is a major pain in the ass.

Imagine a snakefile with the following contents...

rule test:
    output:
        "something.1.txt"
    log:
        "somelog.1.txt",
        "somelog.2.txt"
    shell:
        """
        echo test1 > {output}
        echo test2 > {log[0]}
        echo test3 > {log[1]}
        exit 1
        """

...If you run this locally, you end up with "somelog.1.txt" and "somelog.2.txt". "something.1.txt" will get deleted because the shell script raised a nonzero exit code. If you run it with tibanna, none of the files are uploaded to aws at the moment. Ideally, "somelog.1.txt" and "somelog.2.txt" would both be uploaded to more closely match local expected behavior.

I'm not sure if this is the right place to post the issue. As is, I went ahead and posted this on both tibanna and snakemake. I'll happily close one upon being informed that it is in the wrong place.