Fastq generation and QC: add option to inject local setup script into job scripts

[pjbriggs]

Proposal to add an option to allow a local setup script to be injected into the head of the job scripts in the QC pipeline code.

This could be used to set additional environment variables or perform other actions (for example, this would have been useful to add a workaround for recent automounter issues at UoM).

Implementation would require an update to the pipeliner code (specifically the PipelineCommand.make_wrapper_script() method) and enable the script path to be passed somehow when invoking the method from the PipelineTask.run() method).

The auto_process_ngs infrastructure would also need updating, to allow the external setup script to be specified (either via the command line for the make_fastqs and run_qc commands, and/or as a new config option) and then passed to the pipeline at execution time.