Consider removing --directory argument to snakemake

[rekado]

We are passing --directory to snakemake:

pigx-common/common/pigx-runner.in

Line 389 in 502f8ad

"--directory={}".format(config['locations']['output-dir']),

This option is used to tell snakemake the directory it should use when resolving relative file names in the workflow. Our workflows aren't using relative files, though. We are using absolute file names wherever possible.

When --directory is passed, Snakemake goes crazy when copying workflow files to AWS via Tibanna. On every new job it keeps going one level deeper, looking for config.json relative to output, then output/output, then output/output/output, etc. (This is when the --directory argument is $PWD/output.)

We should test our workflows without this option, both in cluster execution mode as well as local execution.