now evals peak_runnable->run properly. corrected get_alignment_files_by_ResultSet_formats calls, currently forces bam format. Corrected scalars_to_objects calls
added some more parameter validation in the constructor. Corrected program_file attribute naming and init_files call
corrected -z flag spec and file_info assignemnt order
Changed fastq_file param to query_file. Changed reference_file to target_file. Now evals aligner->run properly.
correct get_Experiment call in get_Experiment. Corrected support dereffing in get_Experiment
Corrected $out_dir checking in get_output_work_dir_methods. Improved logging in branch_job_group
Move along, tiny doc change
removed an InputSubset hack which supported InputSubsets before they had a dedicated adaptor
Many changes, debugged and running
many changes, debugged and now running
Added update and overwrite modes to store_tracking_info. Noted how we can convert set_download_status_by_input_subset_id to use store_tracking_info
added default chunk size for split_fastqs, fixed checksum param setting in process_sam_bam. Fixed $conv_method calling in get_files_by_formats. Fixed sam2bed args