Replaced jamm with peakranger for valid peak calling tools.  Added path as optional param for arguments.

Added file_type to argument_keys.  Added file_list_keys for validating inputs/additional_inputs/outputs.

Added 'list' argument to allow vararg inputs. Updated workflow_module & job accordingly to handle new input type.

Add .bam for result and .narrowPeak.gz for bed file types.

Add conf.py entry for the number of result file lines to use for
each document in the bed and peak collections.

Updated workflow_job validation.  Added rawfile type.  Added gem wrapper script, yaml, and chromsome conversion script.

Added db_save_results yaml job, and script.  Updated workflow information tracking to create correct meta data files for saving information to the database.  Conf adjusted to support yaml files, and arbitrary result files.  workflow_job can now return a dictionary of all arguments used.

Added bed & peak file saving functionality to the database class.  Updated testing script to use unittests.  Updated experiment_from_samples script to only print out unique values.  Added list of current tools to conf.

Updated peak_call yaml & jobs.  Fixed r_spp wrapper to handle bad argparsing.  Updated conf to include list of system commands.

Updated conf to include tagalign files.  Renamed script files from wrappers.  Added cat_spp for ungzipped results.  Updated peak_call.yaml to rename .bed files to .tagAlign for spp.

Updated stdout & stderr redirection.  Includes adjustments in individual job yaml files, module yaml files, and workflow generation handling.

Fixed minor issues in param yaml scripts. Updated workflow to add jobs and create relevant pegasus information.  Workflow can now generate download and alignment jobs, still needs testing.  Setup updated to include job-scripts.

Added genome validation.  Added module loading with minor validation.  Added required file detection in modules.