Merge pull request #259 from js21/pipeline

Unmapped reads are now merged by default when mapping with tophat
remove temp assembly directory
remove temp directory before assembly
Merge pull request #260 from andrewjpage/assembly_intermediate_file_cleanup

Assembly intermediate file cleanup
add index to lane.acc
Merge pull request #261 from andrewjpage/add_index_to_lane_accession

add index to lane.acc