Save stdout and stderr logs from active session script usage

[stevekm]

One of the advantages of submitting jobs to the HPC cluster to run with qsub is that the stdout and stderr gets logged; this is not the case when running the scripts in the active session. To get around this, need to look into a method to use tee or similar to catch all stdout and sterr printed to console when running the pipeline scripts 'interactively' so that these logs can be created.