Initial commit of cleaned up BLAST_makeflow.
Added sample files, cleaned up cat_bwa.pl, and converted bwa_makeflow to take strings for inputs.
Removed extraneous files in commit.
Cleaned up files and moved to properly named directory
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
Script creation integrated into BLAST_makeflow
Cat_blast error fixed
Moves writing of Makeflow to seperate function
Moved writing of makeflow to seperate function
Merge pull request #317 from nhazekam/bwa_makeflow

First commit of Makeflow implementation for BWA.
Merge pull request #293 from nhazekam/blast_makeflow

Cleaned up version of the Makeflow implementation of BLAST.
Add -Dfile to show parsed dag, for debugging, mostly.
fix whitespace
add -Dfile to manpage
Write in dag_file only special and exported variables