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
check file regex before sending file to samtools
optimise filter lanes
Update memory for farm3
Merge pull request #248 from andrewjpage/speedup_snp_calling_run_pipeline

Speedup snp calling run pipeline
check if rusage has been set before adding it
extra bracket
Merge pull request #249 from andrewjpage/lsf_memory_increase

Lsf memory increase
copy and paste in assembly.pm
Merge pull request #250 from andrewjpage/fix_assembly_pipeline

copy and paste in assembly.pm
change gc depth for bamcheck in mapping pipeline
Merge pull request #251 from andrewjpage/fix_bamcheck_mapping

change gc depth for bamcheck in mapping pipeline
dont require .body for mapping
Merge pull request #252 from andrewjpage/remove_mapping_requirement_for_body_file

dont require .body for mapping