Options to replace input with output of job

[jnioche]

The jobs currently generate a new seqfile. it would be great to have a '-r input' option to replace the input with the output if the job is successful. We'd also have a '-i input -o output' for the current behaviour

[butlermh]

This commit adds this functionality https://github.com/butlermh/behemoth/commit/87ce262e9f41a07d1025c98790dcb3f9870591b2