Changelog
Follow up on the latest improvements and updates.
RSS
Workflow arguments could previously be set as type boolean, but a user could provide a string as the value. Where a user provided a string for a boolean type argument, we previously interpreted the argument as
False
, regardless of the string content. This update evaluates the string. If the value of the string is "true" (or a variation of capitalizations of "true"), we will now evaluate this as the boolean True
. New
- We've just implemented the ability to download a subset of reads based on the taxa that they have mapped to, through the web application. This utilizes our subset reads script from the One Codex python library, to generate a FASTQ file containing only the reads that map to the selected taxon. You'll find this feature in the complete results table on a sample's classification results page. Note:This is only available on premium samples, to users with the permissions to download the raw FASTQ file for the sample.
New
- We can now detect Element Aviti sequencing data upon validation, and automatically update the sample's metadata with the sequencer information.
- Element, and Element Aviti have been added as sequencer options in the metadata editor modal.
Fixed
- Workflow output files beginning with .will no longer be stripped of their.. Only files with./will be stripped of the./. (Example,.nextflow.logwill no longer be stripped of the leading.).
- ocx.Jobs.getnow works in the experimental onecodex API
New
We've released the newest One Codex Database! Notable changes over the previous database include:
- the addition of new hosts. We've added the chicken and rat genomes to the database, for users working with microbiome samples from these hosts. We've also added the new telomere-to-telomere (T2T CHM13v2.0) human genome assembly (in addition to the hg38 assembly that was present in previous databases).
- Updated taxonomy to capture newly-classified taxa.
- Improved flu specificity, with many more flu genomes
- addition of more metagenome-assembled genomes (MAGs) from diverse studies
New
- Added file_detailsAPI endpoint; which returns a list of files produced by a workflow, and details on those files, such as "filename", "size", and "url".
- PacBio Revio and Onso sequencers have been added as sequencing platform options on the metadata editor menu.
Fixed
- Accounts that only contained pre-upload samples (e.g. only in progress One Codex sequencing samples), did not display the pre-upload samples. This has been fixed, which allows such accounts to view and edit metadata on pre-upload samples.
- Files with fastq.gzextensions can now be chosen when selecting files to upload on the upload page. Previously they were un-selectable (but still uploadable via drag-and-drop and command line).
- When using the Quick Compare tool, filtering the view to a specific taxon, and then changing the taxonomic rank, previously did not display the option to remove the filter. This has been fixed so that we display which taxon the plot has been filtered to, regardless of taxonomic rank, and allows you to remove the filtering.
fixed
improved
Metadata types display fix, and asset unique IDs
- Fixed the displayed metadata "type" on U.I. metadata editor. Previously, though we stored metadata as various types, many types were displayed as "text". Now their correct type is displayed.
- We're now displaying an asset's unique ID on the workflows assets page.
- Project permissions have been updated, so that users within an organization can move samples belonging to other members of your organization between projects.
- The cost for each user-created Workflow run is now displayed at the bottom of the run's results page.
Classification Results Plots Updated
- The tree view on classification results pages has been replaced with a Sankey style view.
- Sunburst plots on classification results pages are now configurable. Font size and zoom options are available, allowing for improved plot exportation.
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
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