Added sample files, cleaned up cat_bwa.pl, and converted bwa_makeflow to take strings for inputs.
Removed extraneous files in commit.
Removed large example files, will replace with smaller files in later commit.
Added copyright information. Removed .pl from cat_bwa.
Slight modification to the cat_bwa header comment.
BWA_makeflow now creates cat_bwa and fastq_reduce internally
Actually included bwa_makeflow in this commit
Revised bwa_makeflow to remove scripts if they exist
Moved writing of makeflow to seperate function
Merge pull request #317 from nhazekam/bwa_makeflow

First commit of Makeflow implementation for BWA.