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Releases: c3g/freezeman

Version 4.6.0

30 Nov 20:12
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  • 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

24 Oct 05:36
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  • Change the ordering on the selection tab of the labwork steps to container name instead of container barcode.

Version 4.5.1

12 Oct 14:11
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  • Fixed an issue that led to Normalization failure when submitting samples with a 0 ng/uL concentration.

Version 4.5.0

10 Oct 19:22
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  • 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

14 Sep 18:16
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  • 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

21 Jun 20:24
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  • 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

24 May 05:13
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  • 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

16 May 18:02
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  • 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

04 Apr 20:04
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  • 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

21 Feb 18:55
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  • 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.