Changelog
Follow up on the latest improvements and updates.
RSS
New
- We've added a metadata editor interface for genomes. You can now edit genome metadata and set a genome's taxon on your genomes page.
Fixed
- We've addressed an issue that prevented consistent default sorting in the Complete Results Table for a sample's classification results.
improved
Alignment Run updates
We've made some recent updates to alignment runs and the viewer for their results.
Improved
- We've improved how we choose a reference assembly to align against. Where previously we selected the assembly with the highest N50, we now select first by assembly category (Representative Genome > Reference Genome > other genomes), then by assembly level, then by N50.
- We now display contigs that have 0 reads aligning to them, as opposed to filtering out those contigs.
Removed
- We've removed the "Width stats" image (cumulative barplot) from Alignment Run results pages.
Improved
- Draft workflow runs did not previously show in the API or the Analysis Dropdown menu. These are now accessible, similar to non-draft workflow runs. They are only accessible by the user who initiated the draft workflow run.
- On the page showing your list of workflow runs, we've removed the status column and merged it with the view button. Successful workflow runs will now show "View Results", unsuccessful workflow runs will show a red "Error" button, and pending workflow runs will show a "Pending" button.
- Any workflow runs that were run using a draft version of a workflow will now indicate "DRAFT". This will show when viewing your page of workflow runs; the word "Draft" beside the "View Results" button. It will also show if you are viewing the results of a workflow run that had any dependency workflows which were in a draft state when run. The "Dependencies" panel of the results page will show the word "Draft" beside any such workflow.
Fixed
- We now convert metadata sheet column names to strings, to prevent errors on importing metadata or sequencing sample registration if a column name is numeric.
- For genomes that had either 0% completeness or 0% contamination, we previously did not display the value in the Assembly Summary table if it was 0. This has been updated so that we now show values even if they are 0%.
new
improved
fixed
Assemblies, exports, workflows, and bug fixes
New
- In cases where multiple assemblies have been associated with a genome, users can now view the different assembly versions, using the drop-down menu at the top-right of the genome view page.
Improved
- Exporting alpha diversity Custom Plot data now includes the metadata field that was used to facet the data.
- Updated default image used for script-type workflows, to an image that has the onecodex python library pre-installed.
- Exporting a Complete Result Table for a classification result now provides up to four decimal places for the estimated abundance, as opposed to the previous two. This now provides the same precision as can be viewed on the Complete Results Table on the browser.
Fixed
- When filtering on the Samples page or the Genome Library, removing or changing the filter will now reset the sample selection.
- Fixed a bug that prevented users from performing actions on pre-upload samples (editing tags/sharing/metadata and downloading metadata)
- Fixed a bug that prevented the "Run" button from displaying for workflows which have parameters and had already been run on the selected sample, but can be rerun. Now displaying a "Run" button as well as a "View" button for such workflows.
- Fixed a bug that prevented users from providing zero or negative numbers when inputting parameters of type number.
New
- Users with the Genome Library feature can now search across their genomes for a gene name or gene ID, to find all of the genomes that have a gene with that name or ID.
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
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