Changelog
Follow up on the latest improvements and updates.
RSS
New
- Released new sequencing dashboard at https://app.onecodex.com/sequencing/dashboard with updated UI, including new columns, summary counts, and a chart for turnaround times of recent samples.
Fixed
- Fixed MLST results API schema to return correct data structure with panelResultsandmlstResultsfields
- Updated references page for Targeted Loci Database, to include 6,109 previously missing taxa and 12,031 new (tax_id, locus) combinations that are contained in the database but were not displaying on the references page.
Improved
- Classification runs with "no reads classified" error now automatically fail dependent child analyses, preventing downstream tasks from processing incomplete data
Fixed
- Shannon diversity on the Quick Compare page was previously calculated using a log base 2. This has been updated to use log base e (natural log), to be consistent with other tools (e.g. client library, Custom Plots).
- We fixed an issue where users whose login had expired appeared to still be logged in. They will now be logged out.
- We fixed display issues for classification results for samples with very few microbes. Previously, is a sample had very few microbes, the "donut" chart display was truncated. Likewise the taxonomic tree displayed just the root node.
- We fixed an issue that prevented exporting a table of Twist results for samples.
- We fixed an issue whereby some password manager extensions prevented adding other users to a project.
Improved
- We now link to the One Codex Taxonomy Time Machine (https://taxonomy.onecodex.com/) from the references page (https://app.onecodex.com/references). This will improve searching for older or alternative names for taxa.
Improved
- We've improved our importing of large files. We can more reliably estimate the expected size of the file and provision appropriate space for import/validation, resulting in fewer retries, and overall faster processing.
Fixed
- Fixed error when loading samples with multiple dependencies in API v1 endpoint.
fixed
API
Paginated sorting consistency
Fixed
- We fixed a pagination-related sorting bug, whereby sorting by non-unique fields, such as "created at", could result in samples shuffling between pages. Sorting will now be deterministic.
Improved
- It is now possible to save the "donut" chart from classification results pages.
improved
Organization invitations update
Improved
- When inviting a user to join an organization, we no longer automatically add the user to the organization. Instead, the user is sent an invitation, which they need to accept prior to them becoming a member. The invited user will show as "Pending invitation" on the organization's members page.
Fixed
- We've fixed an error that prevented filtering with nested IDs via the API. e.g. where={"sample": {"id": 123}}
- When viewing a report's results page, clicking the "Download" button now immediately generates the download, instead of redirecting to the PDF viewer.
- We've added support to workflows for Nextflow schema union types e.g. ["boolean", "string"]
Improved
- We've reduced the minimum % of reads threshold for a taxon that users can search across samples to 0.0%. This allows searching for samples with low but non-zero read counts for a taxon.
- We've added OCX_INSTRUMENT_VENDORas a possible variable for workflows. This populates with our sequencing instrument vendor detection step run during sample validation, and is saved to a sample's metadata. Current value options are "Illumina", "Oxford Nanopore", "Element" or "Ion".
- We've increased the export capability for long .csv format. More samples can now be exported in one file.
fixed
Client Library
onecodex version 1.0.1
Fixed
- Samples without abundances were filtered out of heatmaps and stats functions when using non-abundance metrics
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