One Codex

Changelog

Follow up on the latest improvements and updates.

RSS

improved

fixed

Filtered readcounts, workflow runs loading performance, cookie banner

Fixed
  • For samples for which we were unable to estimate abundances using the One Codex Database, we previously displayed unfiltered readcounts, which was not directly comparable to the filtered readcounts displayed for samples that abundances could be estimated for. We now provide the filtered readcounts for both samples that failed to estimate abundances and samples that succeeded.
  • Renamed API schema fields from
    unfiltered_readcount
    and
    unfiltered_readcount_w_children
    to
    filtered_readcount
    and
    filtered_readcount_w_children
    to provide consistent metrics.
  • Updated Custom Plots to use
    filtered_readcount
    metrics and removed deprecated
    unfiltered_*
    metrics from the metric dropdown menu.
  • Updated embedded One Codex client library to match schema changes
Improved
  • Added performance improvements for slow loading on workflow runs page.
  • Updated cookie consent banner.

fixed

Comparison sample loading fix

Fixed
  • Fixed loading of samples in classification comparisons.

improved

API

Samples API performance

Improved
  • Improved performance of samples API calls with S3 client caching.

new

improved

API

Draft job visibility, assembly search performance

New
  • Side Panel in Workflow Editor is now collapsible.
  • Users can now see their own unpublished draft jobs in the jobs API endpoint, with a new draft field to distinguish them from published jobs.
Improved
  • Improved performance of searches for assemblies, e.g. when searching for an assembly to align a sample to in the alignment workflow launch page.

fixed

Quick Compare fix

Fixed
  • Fixed Quick Compare loading error.

improved

fixed

Launching analyses improvements

Improved
  • Workflow submission now supports up to 500 samples (increased from 250)
  • Improved interface for workflow submission, with progress indicator showing "X of Y submitted" during batch processing, and navigation confirmation to prevent accidental page exit.
Fixed
  • Fixed various page layout and display issues.
  • Trailing whitespaces are now trimmed from analysis job names.

fixed

API

Custom Plot exports and corrected error types

Fixed
  • PNG/SVG export now works correctly on distance heatmaps in custom plots
  • API now returns 400 errors instead of 500 for malformed
    ?sort
    JSON and filtering on non-filterable schema fields

new

improved

fixed

Workflow SHA, Custom Plots, and various bug fixes

New
  • For custom workflows, we now fetch, store and verify the commit SHA corresponding to GitHub/GitLab tags.
Improved
  • Custom plot titles now truncate with ellipsis when they exceed container width instead of overflowing
Fixed
  • Custom plots now provides clearer feedback when connectivity issues occur
  • Fixed exporting multiple functional results that could time out due to empty table handling
  • Fixed ability to copy old demo notebooks

new

improved

Workflow options and improvements

New
  • $OCX_CPU_REQUEST
    variable now injected into Custom workflow environment so that job scripts can now access the number of CPUs requested by the workflow.
  • Workflow environment variables
    $HOME
    and
    $USER
    are now set to more sensible defaults.
Improved
  • Canceling Nextflow workflows with child tasks now cancels the child tasks, instead of waiting for them to finish.

new

fixed

API

Job details, deleting assets, and various fixes

New
  • Added
    /jobs/{id}/details
    endpoint to API to expose job assets, dependencies, script, image URI, and other details with appropriate permission checks
  • Added ability for organization admins to delete unused assets from the Assets page
Fixed
  • Fixed search suggestion type from being unclickable
  • Fixed display of x-axis labels in Quick Compare charts
  • Fixed trimming on repository URLs in job editor page. Excess whitespaces will now be trimmed prior to URL validation.
  • Fixed various display issues.
  • Improved error message for Custom Plots when insufficient memory is available.
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