blast flag is ambiguous...really this should be for saving temp files to a known place.
separate the save_temp flag from the use of intermediate.
renamed this intermediate file to be consistent with the others.
more informative file name
use_temps flag instead of velvet flag
forgot to declare $contigs_file
wrong check
really there should be two flags, noblast and noassemble.
Merge pull request #71 from juliema/temp_files

Changed -velvet flag to -noblast, added a corresponding -noassemble flag.