Changelog
Follow up on the latest improvements and updates.
RSS
New
We have released v0.18.0 for the onecodex library. This includes the following updates:
- Adds ocx.FunctionalProfiles to fetch functional analyses results
- Adds SampleCollection.to_classification_df()andSampleCollection.to_functional_df()methods to return classification or functional results as DataFrames
- Adds option to omit taxonomic labels from plot mappings
- Ensures singleton FASTQ filenames follow the same format as chunked uploads (Oxford Nanopore)
- We fixed an issue with onecodex login requiring an API key for certain accounts. Users should now be able to login via the onecodex CLI without providing their API key in the login command.
Improved
- Functional runs have been promoted to a full v1 API resource, and are no longer restricted to the experimental flag.
- You can now set default values for workflow arguments on workflow creation/edit. Note that this is not currently permitted for arguments of type sample,assembly, orgenome.
Fixed
- For users in a One Codex Organization, we've fixed a bug that prevented inviting users to organizations if their email casing differed from the user's registered email.
Improved
- Alignment workflows now allow you to choose a genome to align to from the run confirmation page. Assemblies which are reference assemblies for the organism are marked with a checkmark for easier identification from the list of assemblies/genomes for that organism.
New
- You can now choose to include a sample, assembly or genome as an input argument to your workflows. sample,assembly, andgenomeare available as argument types when creating/editing your workflow. When launching workflows with an argument of typesample, you will be able to choose from the samples available to you through a dropdown menu. Arguments of typegenomeorassemblywill allow you to search for genomes/assemblies by name, based on names from genomes we have imported from GenBank. If you are a Genome Library customer, you can alternatively choose your own genomes/assemblies.
Fixed
- Analysis file sizes are now returned as intinstead offloatthrough the API.
Improved
- We've improved the view for alignment runs. Now you can click on locations in the Contig order, which will zoom in to that view on the Pileup View.
New
- We've added a webhook event for when sequencing samples are received at our lab.
Improved
- We've updated the API response for AlignmentRunresults, providing more valuable output metrics, such asaverage_coverage,median_depth, andaverage_identity, among others.
Fixed
- We've fixed a loading error that resulted in a complete results table for a sample's classification results not refreshing when loading another sample.
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.
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