Fixed the run_single_analysis and job_submission_command methods to allow the passing of commandline-specified $output_dir from test_single_analysis.pl to jobs.
Fixed the run_single_analysis and job_submission_command methods to allow the
passing of commandline-specified $output_dir from test_single_analysis.pl to
jobs.

Ensembl/ensembl-pipeline,Ensembl/ensembl-pipeline,Ensembl/ensembl-pipeline