GitLab

Updated 3 things: 1st changed pepr arguments to be a list with a separator.  Updated argument parsing to allow joining list arguments with another value.  Updated conf to allow separator as a valid argument option.

Job argumnet creation is now actually legible AND works with the new style of inputs/outputs as well as job definition files.

Heavily updated workflow_job parsing & validation.  Addeded several tests to confirm the validity of new parsing.  additional_inputs no longer exist, and input / output files are defined as dicts instead of lists.  References refer directly to the dict key names instead of a list index.

Updated workflow parsing to require a properties file.  Executable loading is now done based on the provided chipathlon_bin path.

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.