Merge pull request #206 from nds/add_sga_step_to_pipeline

Send pe_mode argument and also separate the output_filename and director...
Get rid of extra double quotes
Merge branch 'pipeline' into virus_assembly_spades
Merge branch 'pipeline' into add_primer_removal_to_pipeline
Change default QUASR exec path
Merge branch 'add_primer_removal_to_pipeline' into virus_assembly_spades
Clean up the files produced by primer removal
Merge branch 'add_primer_removal_to_pipeline' into virus_assembly_spades