Changelog
Follow up on the latest improvements and updates.
RSS
New
- It is now possible to download assets via the experimental API, using the download_uriroute to the Assets resource.
New
- Any custom Workflows that use dependencies can now have their dependencies overridden at the time of launch via the API. See the dependenciesproperty in the jobs schema. If overriding a dependency, the run you specify must already exist, and be run on the same sample as you are trying to launch the child workflow on. The dependency run does not have to be completed yet. As with other dependencies, overriding dependencies cannot be in a draft state if the child task is in a published state.
Improved
- Exporting the long-format results table for samples previously provided "Relative Abundance" in column I, which was the abundance estimate at species level. This did not provide abundance sums at higher taxonomic ranks. We have since updated the long-format export to now provide "Abundance with Children" instead. This provides not only abundances at species level, but also the sum at higher taxonomic ranks.
- When viewing alignments that have been run for a sample, we now display the genome's name and unique ID on the alignment overview card. This should allow users to distinguish between alignments run against different assemblies for similar taxa.
- Sorting samples by date will now sort completed sequencing samples based on the date that they completed. Any in-progress sequencing samples will still be sorted by the date that the sample was registered or arrived at the lab if not registered.
Fixed
- For BaseSpace BioSamples, we previously identified files stored under common.fastq. Some users files had not been stored in this location in BaseSpace. We now search under bothcommon.fastqandcommon.files.
- For panel results, clicking to download the table incorrectly generated complete results file in .json format. This has been corrected and now provides only the table in .csv format.
New
- You can now filter your samples list to show your sequencing samples that are in progress, and filter them based on their status.
Fixed
- Using the init_uploadendpoint for paired-end files returned an incorrect key, missing theR1andR2from the filenames. This has been updated.
Fixed
- You can now launch workflows on samples in your organization that are not owned by you nor explicitly shared with you.
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.
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