oops, coveralls never checked tools.* previously, so add that to .travis.yml
rmdup needs to operate on all reads at once [ci skip]
fixes and additional all_deplete rule [ci skip]
fix wildcard expansion [ci skip]
alter LSF priority for chokepoint in DAG [ci skip]
fix split_reads pipe call [ci skip]
add some early scratching at demux. make assembly_reports robust to old reports being there. [ci skip]
clean up some welcome message stuff
some cleanup to samtoolstool
distribute bmtagger more, blast less. break refine_assembly_with_reads into two steps. more bamstats for more bams [ci skip]
tweak LSF params [ci skip]
much more pipes [ci skip]
oops, forgot this [ci skip]
clean out unused code and command line calls to tabix
fixes and tweaks to ref_guided rules
more cutting of unneeded code
reduce runtime for ref_guided_diversity [ci skip]
Merge pull request #46 from broadinstitute/dp-demux

basic pipes and reports for first batch of data