Asm module

[karinlag]

• [x] Don't export-save input files
• [x] Fix dummyar
• [x] Export log file for trimmomatic
• [x] Clean up output names, i.e. don't have them as params
• [x] Check that all output files go where they should, esp quast.
• [x] Fix BBMap, understand what is happening
• [x] Add prokka
• [x] Add pilon
• [x] make process names uniform, see spades