filter out lanes which have already been mapped
speedup mapping by not generating coverage data thats not used
no need to check if mapping done twice
Merge pull request #241 from andrewjpage/speedup_mapping

Speedup mapping
Deal with single cell reads differently when getting kmer sizes
Merge pull request #242 from martinghunt/single_cell_assembly

Deal with single cell reads differently when getting kmer sizes
Only run --assemble-only when the spades assembly is not single cell
Merge pull request #243 from martinghunt/single_cell_assembly

Only run --assemble-only when the spades assembly is not single cell
Updated pseudo_genome task: requesting 2 procs and spanning 1 host.
Merge pull request #244 from fy2/pipeline

Updated pseudo_genome task: requesting 2 procs and spanning 1 host.
Cleanup more directories from SPAdes assembly
Merge pull request #245 from martinghunt/single_cell_assembly

Cleanup more directories from SPAdes assembly
SSPACE and GapFiller accept number of threads
Fixed comment
Merge pull request #246 from nds/add_threads_to_sspace_and_gapfiller

Add threads to sspace and gapfiller
add user params for tophat
Merge pull request #247 from CraigPorter/user_tophat_params

add user params for tophat