Changelog
Follow up on the latest improvements and updates.
RSS
You can now export One Codex Database classification results using the CSV "Long-Format" export for up to 10,000 samples at one time.
The "Long-Format" export represents a sparse matrix of taxonomic classification results, with each row containing a result for a particular sample and taxon pair.
new
improved
API
Sequencing Dashboard and Analysis API Updates
Sequencing dashboard and API improvements
- The default sample format for new sequencing orders is One Codex Reformatting Tubes - this is just a visual update since this is the sensible default for most users.
- Added a set of API endpoints at /api/v1/sequencing/batchesfor registering sequencing samples and batches programatically
Updated timestamps for
Analysis
API resources- Analyses(and the various subtypes) now expose anupdated_atfield in the v1 API schema
- This can used in conjunction with API filter parameters to get analyses updated since a certain time
fixed
improved
Client Library
One Codex Client Library v0.16.0 Released
Added
- Adds optional secondary_haxis parameter to plot_metadata(), which can be a field name or tuple of field names, if a second grouping is desired
- Adds alpha diversity stats tests, which are run via SampleCollection.alpha_diversity_stats()
- Adds support for Python 3.12
- BIOM export now includes canonical taxonomic lineage
- Adds documentation via GitHub Pages at https://onecodex.github.io/onecodex/
- Adds support for concatenating ONT files
Changed
- Adds scikit-posthocs dependency
- Pins scikit-bio to 0.6.0
- Updates minimum required version of scipy to 1.11.0
- Updates minimum required version of numpy to 1.21.6
- Pins pydyf<0.11.0
Fixed
- Fixes a bug associated with updating custom metadata on a sample
- Fixes metadata non-unique column name bug
- Provides a more useful error message if plot_heatmap is called with any samples without abundances calculated
- Fixes abundance chart for groups of samples where all samples lack abundance estimates
Removed
- Removes Python 3.8 support
With default settings, Oxford Nanopore sequencing instruments will split their outputs into FASTQ files with up to 4000 sequences each. This meant users with ONT sequencers had to manually concatenate these files for each barcode before uploading to One Codex.
Now, we will try to detect when you've dropped partial FASTQ files into our drag and drop uploader and will automatically concatenate these files for you!
We've also added this behaviour to our One Codex CLI, so if you have a folder of files from a MinIon or other ONT sequencer, we'll parse out which files belong to which barcodes and automatically concatenate the different parts.
We now expose an error message for samples that failed to import or validate successfully in a new
error_msg
field on the /api/v1/samples
and /api/v1/samples/<uuid>
endpoints.We are also now exposing more specific error messages in the One Codex application as well when a sample fails to import or validate.
The workflow orchestrator powering all One Codex workflows is now build atop the Task Execution Schema (TES) defined by GA4GH. For Nextflow Workflows, these are now executed using the TES executor for Nextflow.
For our users, this means you should see more reliable and faster analyses, with fewer spurious Workflow execution failures, more parallelism, and support for even greater scaling than before.
Previously, you could only run a given
Workflow
once for a particular Sample
. You can now kick off a Workflow
as many times as you want on the same sample, as long as the chosen parameters are different.- Added a job_argsfield to the/api/v1/analyses/<uuid>endpoint, which will contain the hydrated dictionary of arguments passed to theAnalysis
- Added a job_args_schemafield to the/api/v1/jobs/<uuid>endpoint , which contains the JSON schema for arguments that can be passed to that Workflow
We just launched a complete redesign of the Run Workflows page in our web application. Now, instead of having different tabs for your workflows versus the built-in workflows, you have a unified view of all available workflows.
The new design makes it easier to find and run exactly the workflow you're looking for, with options to show recently run workflows, draft workflows, and either all available workflows or just your organization's workflows.
The new and improved analysis switcher!
In the analysis dropdown, workflow run rows are expandable:
- Non-default argument names and values are displayed, sorted alphabetically by argument name
- If there aren't any non-default arguments for a run, the row isn't expandable
- Multiple rows may be expanded simultaneously, and expanding a row doesn't navigate away from the current page
- Longer argument names and values are truncated with ellipses and have tooltips to see the full content
- The dropdown menu grows vertically until it reaches the bottom edge of the window, then it becomes scrollable
- Added created_at date to each analysis item in the dropdown menu
We also fixed some bugs:
- If multiple analyses exist from the same job, newer runs are now displayed first. Previously, the ordering in the list would arbitrarily change if you selected an analysis.
- The Arguments section of the Workflow results page now displays boolean arguments correctly. Previously, boolean argument values were hidden.
SSO Support for Microsoft Entra ID
We now support single sign-on for customers using Microsoft's Entra ID! If you already use Entra ID and would like to set up single sign-on to One Codex for your team, get in touch. This adds to our existing support for Google, IdentityServer, and OpenID connect-compatible identity providers.
Other fixes and improvements
- Previously, when you would update the repository URL or tag for a Nextflow workflow definition, we would silently re-fetch the Nextflow schema for the workflow. This could lead you to unintentionally lose updates you'd made to the schema in One Codex, so now we warn you before re-fetching the schema
- We now display completeness and contamination statistics on the overview page for a genome in your Genome Library
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