Version 4.6.0

• Create a Automated step to create folders for Axiom.
• Create a Integrated QC step for the Spark instrument that reads a result file to complete an Axiom QC.
• Create an Experiment run step for Axiom.
• Create an Axiom workflow.
• Create an Infinium workflow.
• Added a definition section page to list the existing instruments in the system.
• Allow partial sample and library QC to be submitted. Only one flag and instrument is required for the template to be accepted.
• Allow creation of containers using only a Barcode identifier, using the barcode as name in those cases.
• Reorganized the listed indices for easier usage by the lab in the sample submission and library preparation templates.

Version 4.5.2

• Change the ordering on the selection tab of the labwork steps to container name instead of container barcode.

Version 4.5.1

• Fixed an issue that led to Normalization failure when submitting samples with a 0 ng/uL concentration.

Version 4.5.0

• Added an optional description to the Study.
• Added a way to bypass NA input requirements for normalization planning step.
• Fixed an issue with individual parent not being possible to remove using the individual edit form.
• Validate the sex of individual parents (mother => F or U and father => M or U).
• Reworked Data release to work around readsets instead of files.
• Added run metadata to the readset release form.
• Corrected format of ingested json from run processing (addition of file size, moved project_obj_id).
• Created differentiated step for Normalization (Genotyping) in order to split workflows correctly for genotyping and sequencing.
• Created new step for performing the sample preparation for Axiom workflow.
• Parent containers can be seen in the labwork section of the the application in order to better validate tubes used.
• In labwork and project steps listings, a new Samples in pool column was added to know at a glance how many samples are in a pool.
• Added more columns to be prefilled in the popup presented for Extranction, Transfer and Normalization steps.
• Indice validation form no longer offer validation for instruments that are not in the system.
• Added ordering by NCBI ID and Name in the Taxon list, italicized the taxon names, and limited the taxons by page.
• Changed the default ordering of endpoints to provide more likely items to the user when listing entities (changes the application default list ordering).
• Pooling template now has more sample lines formatted and no longer always have volume in pools with decimal positions.
• Sample extraction template has more sample lines formatted.
• Fixed an error message when the parent container in a template was different than the one stored in Freezeman.
• Sample submission template now uses "Individual Name" instead of "Individual ID" to better match other instances of the field name.
• Added coordinates references on the index page of Normalization and Normalization Planning templates.
• Refactor of Indices, Users, Individuals, Containers, Libraries, Samples tables.

Version 4.4.0

• Added to Extraction, Sample QC and Normalization Planning templates columns to locate the sample containers (notable the tubes) in their parent containers when prefilling the template.
• Run metrics report now opens in a new tab.
• Reference Genomes main descriptor cannot be edited once the reference genome is used on an individual.
• Warnings are now grouped in a new section when submitting templates in order to quickly assess them before confirming submission.
• Prefilling templates from the labwork section now provides the option to prefill some columns with a single value for all rows.
• The projects now require an external project ID to be entered during creation unless the user is admin.
• All templates used in a workflow now have a prefilled column with the current sample volume in Freezeman.
• Some templates have the option to use the "ALL" keyword instead of a numeric value to indicate that all volume must be used. Each template info sheet will mention the "ALL" keyword for the column where it is usable.
• Forms now include descriptions of the fields to populate. Some info dots are also added to describe the characters and format accepted.
• When on a labwork step, it is now possible to use the "Select All" button to select all filtered samples across all pages.
• Mandatory column indicators have been added to more templates.
• In the study tab of a project, the number of samples in a pool are displayed for some workflow steps.
• In the associated samples tab of a project, there is a new "Last Protocol" column that indicate the last protocol to be executed on this instance of the sample. It is intended to facilitate the queuing of the correct instance of a sample into a study.
• Fixed an issue with the login.

Version 4.3.0

• Run processing metrics are stored in Freezeman and a new section allows the lab to set run validation flags.
• Adds a menu section for definitions with Taxons, Reference genome, Workflows and Indices listed. Taxons and Reference genome can be edited.
• Lists samples that are tied to an individual in the individual detail page.
• Adds advance search to the container listing that allow to search containers by Comment field content.
• Allows to remove study that have no sample associated and that were not initiated.
• Samples removed from study workflows are listed in a separate tab in the section of the last step completed.
• Allows users to remove samples from study workflow from the project study tab.
• Allows ordering of coordinate in descending order for selected samples in the labwork section.
• Filter warning and button to clear filtering on workflow sample tables.
• Sample submission have a new sample type selection column and uses the date in the header to populate dates in rows.
• Addition of libraries that are only processed as ready to sequenced to the available libraries.
• Renames container label to container barcode in sample details view.

Version 4.2.1

• Fixed an issue with sample export returning the internal ID instead of the coordinate name.
• Fixed an issue with the Study samples being limited to 100 in the project tab listing.
• Added Curation commands for deleting containers and deleting samples.

Version 4.2.0

• Coordinates moved to an independent model with both column and row information allowing ordering in each dimension.
• Transfer step added to workflows before each Library Quality Control step.
• Library Normalization step removed from workflows and replaced by expanded pooling template. No longer provides robot files.
• Addition of a completed tab on the project study page for each step.
• Samples that are removed from the workflows are listed on the project study page in their own tab.
• Container creation template now have a comment column to set the container comment at creation.
• Coordinate dropdown auto-complete feature improved to better match user entry.
• New Freezer Rack 16x6 added to the available containers.
• Improved the interface for steps with multiple templates available.
• Improved the message returned when failing to provide the extraction type in the template.
• Improved labwork summary protocol sorting.
• Selected samples in labwork step can be sorted to control prefill order.
• Addition of a project column with filtering to the labwork step.
• Application Initial data loading optimized.
• Application loading code for project study optimized.
• Addition of a dynamic sample kind filter to the labwork step.
• Display step order numeric value before the step names in study workflow description.
• Collapsed and expanded panels in project study are now tracked and remembered.
• Filtering and ordering added to the project study columns.

Version 4.1.0

• Addition of Lab work section :
  • Provides a listing of all samples queued to workflows by protocol.
  • Selecting a step, lists all samples queued to that step and facilitate completion of the step.
  • Cherry picking of samples to undergo each step and enhanced prefilling to add information specific to the current step.
  • Template submission can now be used to move sample along their workflows.
• Steps without any samples can be hidden by a toggle.
• Samples with a volume of 0 uL will now be automatically depleted.
• Addition of qPCR as a Library QC quantity instrument.
• Multiple QoL changes to Sample submission :
  • Principal investigator, project and quote ID cells for tracking.
  • Removed library question. Adding a library type to a line will unlock the library cells.
  • Reception Date column moved to the beginning of the line.
  • Make concentration and collection site optional at sample submission.
  • Allow queueing to multiple studies at sample submission by separating study letters by "-".
• Study listings now refreshed automatically every 30 seconds.

Version 4.0.0

• Sample metadata can now be exported to a csv using the sample section export dropdown menu.
• Workflows created and Database schema changes to support workflows.
• Addition of the study entity. Serve to instantiate workflows in the Project section.
• Samples can be added or removed to a study using the Project and Study link samples template.
• Samples can now be tracked in their study workflow in tabs in the Project section.
• Reference genome added to the individuals representation and is exported to the run_info file.
• Sample submission template now allow the queuing of samples to a study and the choice of a Reference genome.
• Sample can no longer be submitted without a project.
• Added Node.js installation to the DEPLOYMENT.md file.