Merge branch 'release/0.189' into develop
sequenom_import_from_irods_and_covert_to_vcf pipeline now indexes the vcf, and test script updated some test expectations
irods all_with_warehouse_metadata method has new required_metadata option
our_step_numbers() now considers a step to be ours if files were created in our unique hashed dir, even if they were also made by other setups
new merge_metadata() method for File
no longer deletes the intervals file during cleanup
various recent vcf pipelines have the vcf_index step removed and the vcf-producing steps now internally index their output
various recent vcf pipelines have the vcf_index step removed and the vcf-producing steps now internally index their output
sort the merged values
datasourcerole _start_over_elements_due_to_file_metadata_change() now takes a changed_details arrayref so it can log what metadata changed
replace any existing lane metadata with vrtrack-style lane name
meta_value() on an instance with no metadata no longer falls over
do not quit when testing on a single debug setup
new open_irods_command() and run_irods_command() methods that try to run irods commands 3 times before failing; new get_file_metadata() and get_file() has an option to use that to add file metadata to a downloaded file
uses VRPipe::Steps::irods methods to run irods commands; supplies changed details to _start_over_elements_due_to_file_metadata_change; collection picking logic improved
no longer stores undef irods_local_storage_dir metadata when there are no analysis_files; adds merged metadata of parent file to each analysis file, as well as irods metadata
store correct lane hierarchy_name; store the first sample_accession_number we see in individual->acc, not the last
updated test expectations now that some upstream metadata has changed; added some extra tests
get all anaylsis files
fixed several pluritest issues and added metadata to files