TODO.markdown

-Create wrapper scripts for each tool
-Create param files for each tool
-Update peak calling and remove duplicates modules from dummy values
-Code to insert results into MongoDB and GridFS (Python classes and wrapper scripts)
-Create Genome collection in MongoDB
-Create the Modules class
-Pegasus stdout handling for certain tools (bwa, samtools, zcat, sort, etc.)
+*Create wrapper scripts for each tool
+*Create param files for each tool
+*Update peak calling and remove duplicates modules from dummy values
+*Code to insert results into MongoDB and GridFS (Python classes and wrapper scripts)
+*Create Genome collection in MongoDB
+*Create the Modules class
+*Pegasus stdout handling for certain tools (bwa, samtools, zcat, sort, etc.)
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