Option to use Spades and multithreading for Bowtie2 and Spades#210

Merged

martinghunt merged 3 commits intosanger-pathogens:masterfrom ngs-mstb:at_spades

Feb 2, 2018

+914-133

Commits on Feb 1, 2018

Option to run subprocess w/o shell
Andrey Tovchigrechko
committed
Remove reference to spades options in tests that are not using spades.
Andrey Tovchigrechko
committed
Reintroduce Spades as another assembly option. Multithreading for Spades and Bowtie2.
Andrey Tovchigrechko
committed