1.14.3

Legacy maintenance release.

Release 1.14.2

Minor addition: Enable Fluidigm QC results to be published to iRODS

Release 1.14.1

Added Fluidigm QC:

• Compute QC metrics and write in CSV format
• Can update an existing CSV file
• Command-line script qc_fluidigm.pl

Release 1.14.0

• Replace identity metric with Bayesian version:
  • Update QC pass/fail evaluation, plots and reports
  • Bugfix in Utilities.pm: Need to import Runnable
  • Removed identity_qc workflow and tests from Ruby code
• New workflow to write Plink and run gencall QC only
  • Refactored ready_workflow.pl
  • Fixes Text::CSV issue #406
  • Fixes identity argument issue #434
• Extensive refactor of QC metric collation
  • Converted Collation.pm to a Moose class Collator.pm; enables better code structure and use of Loggable Role
  • Replace single collate() method with individual methods to write output files, update pipeline database, etc.
  • Supply only one JSON config file, which determines all thresholds (instead of allowing a filter file to override the config thresholds for the pipeline database update)
  • Use Text::CSV instead of split() to read metric results
• Added tests for dry-run mode of Fluidigm archive script

Release 1.13.2

Hotfix to add manifest paths for Fluidigm in the old identity QC check

Release 1.13.1

• Made install.sh more transparent and portable.
• Updated WTSI-DNAP-Utilities and perl-irods-wrap versions in install.sh. Includes updates to logging.
• Fixed default LSF queue for Ruby workflows

Release 1.13.0

• install.sh script to install pipeline and its Perl dependencies
• Documentation for Bayesian identity check
• Modified ready_workflow.pl to better align with user SOP
• Updated reference genome for Sequenom iRODS query
• Update perl-irods-wrap dependency to 2.4.0; this requires baton version >= 0.16.4.

Release 1.12.0

• New ready_workflow.pl script for pipeline setup
• Improved implementation of prototype Bayesian identity check
• Made compatible with latest dependency versions
• Removed Annotation modules; functionality replaced by Metadata.pm in wtsi-npg/perl-irods-wrap