Changelog
Follow up on the latest improvements and updates.
RSS
Fixed
- We identified an issue whereby clicking to publish an unpublishable workflow deactivated the publish button for other, publishable workflows. This issue has now been fixed.
Many workflows are built with default values for arguments. Upon launch of a workflow on a sample, unless the user provides non-default values to override the defaults, we have automatically populated the values with the default values.
Now, we allow users to determine whether or not default values should be provided, even if the user does not provide alternative values for those arguments. If launching a workflow via the API, users can pass the flag
populate_default_arguments=False
if they wish for default values not to be populated. Otherwise, default values for arguments will be populated. Likewise if launching via the web application, the user may remove the default values for various arguments if they choose to. Note that if users do provide the
populate_default_arguments=False
flag, and an argument is a required argument without a value, the workflow will fail to validate, and will not run.Custom Plots automatically chooses the primary classification for a given sample included in the plot. Some users may have samples which were classified with different database versions, or multiple versions. We've added a field under the Custom Plots image to clarify which database(s) results are being displayed, including the unique identifier for the database version. If multiple databases were used, we will also display the number of samples using that database in the list of databases.
New
- Outputs from failed Workflow runs now persist indefinitely. Previously these were auto-deleted after 7 days.
- We've added an API endpoint to permanently delete output files from failed Workflow runs. This can be reached with DELETE https://app.onecodex.com/api/v1/analyses/<id>/files.
- We now display CPU and memory usage over time for longer running parent shell workflows. (Note this does not apply to Nextflow workflows at this time).
Fixed
- Fixed an error that prevented some functional exports from generating, to allow for rows where no taxon exists.
New
- Added an optional injection of a bearer token into the workflow environment. The bearer token can be used to grant access to the One Codex API from within the workflow execution environment. The option can be selected on the workflow creation and edit screens.
Improved
- We've improved how we select the best reference assembly for alignments
New
- We've added a new API endpoint for sequencing samples. For a specified batch, you can now query the samples in the batch. This returns a list of json objects, one for each sample; including a reference with the sample's unique identifier, as well as the tube barcode.
Fixed
- We removed hyperlinking that did not lead anywhere in Custom Plots x-axis titles, where a Taxa plot is generated using grouping.
Improved
- We now prevent selection of older, no longer supported Nextflow versions upon workflow creation or edit. Existing workflows built on older Nextflow versions will continue to work.
Fixed
- Previously, workflows built on schemas that contained default values populated the defaults if the workflow was launched from the web application. However, workflows launched via the API were not populated with default values. This update now uses defaults upon launch via the API, unless they are overridden.
- Upon completion of a new classification for a sample, the Custom Plots metadata will be refreshed to ensure correct capture of the updated classification, if appropriate.
New
- We now auto-register reformat tubes upon sequencing order fulfillment. Users who order sequencing for samples that require reformat tubes are no longer required to register their batches. However it is still advised to register batches for the purposes of adding metadata to your samples such as a sample name or your own identifier, and for being able to track the processing stage of a batch. Note, this update does not apply to users with OMNIgene Gut tubes, as we do not know the unique identifiers of such tubes upon order creation.
New
Sequencing
- Added a status for each sequencing batch to the sequencing batch API endpoints, allowing tracking of batch status. (Note that batch status is the status of the lagging sample.)
- Added webhook to provide notice on when a sequencing batch has been received at the lab
Workflows
- Added dependenciesinformation into theanalysisAPI endpoint for workflow runs that were dependent upon other workflow runs.dependenciesis a list of json objects for each workflow run that the specified analysis depended upon.
- We now provide an immediate warning if a user tries to create a Workflows argument with an invalid name or a name containing invalid characters. (Note that argument names have always been validated, but users previously were only notified upon submitting the workflow.)
Misc.
- Added functionality to alignment viewer to allow for downloads of the alignment (BAM) file and the reference (FASTA) file for a given alignment.
- Added the ability to download subsets of Functional results from the samples page, using the "Download Selected" menu. Choosing "Functional Results (.csv)" will generate a pop-up modal, allowing users to select which annotation type of their functional data they wish to export. As functional data can be quite large, long-running exports will be emailed to users.
- You can now find a project's unique identifier on both the project permissions and project details pop-up modals. In addition you can copy a project's unique identifier if you have selected/filtered to the project on the samples page.
Fixed
- We fixed a Custom Plots bug where plots were not re-rendered upon removing and re-selecting certain choices (such as a tag)
improved
fixed
ATCC uploads and sample-appropriate analyses
Fixed
- The upload panel for ATCC Discrepancy Reports has been fixed to now allow upload of interleaved or single-end files.
Changed
- The Targeted Loci Database can no longer be run on samples sequenced by One Codex, as these are not generated using an amplicon library preparation approach.
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