TODO.markdown

-* Create wrapper scripts for each tool
-* Create param files for each tool
-* Update peak calling and remove duplicates modules from dummy values
+TODO
+======
+* Update wrapper scripts walltime / memory to correctly reflect request values.
+* Update peak calling and remove duplicates modules from dummy values.
+* Refactor modules code.
+
+Database
+===========
 * 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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+* Job definitions to load data into database
+
+Helper Scripts
+================
+* Script to generate param.yaml file
+* Script to generate workflow with provided inputs
+
+Polishing
+===========
+* Update pegasus stduout/stderr redirection
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