I'm currently producing SAM alignments from NGS data using the 'Map Reads to reference' tool.  All going fine but I still have hundreds to process and wondered if anyone knew any terminal coding to run in bulk or automate.  I also can't seem to get the workflow designer to do it. 
Here is my current workflow:
- Tools - NGS - Map reads to reference
- Select Bowtie
- Identify ref sequence (always the same)
- Import 8 NGS fastq
- Run
- Then I 'export assembly region' to SAM across a defined bp range (Always the same).


Any advice...?
Many thanks :)