intial assembly pipe commit
added / to end of output folder
added extra velvet, spades, ordered and annotations dirs to mkdir
added assemble spades command
added new modules, prokka commands w/ and w/o protein list
added spades assembly and moving spades contigs
edited follows for copying stages and delete scratch
added correct folder to output
fixed walltime bug in config, added extra order, stats, blast steps for spades
adding prokka options
fixed typo
fixed getBest for Spades
fixing bug in order start point

Needed to use sequences instead of tranforming from a previous step
after scratch had been deleted
fixed bug with output of ordered contigs after blasting
added prokka framework
fixed but with output contig folders
config for prokka test
changed regext input for copyProkka files steps
removed extra slash in out ordered prefix
added force to prokka commands