One Codex

Changelog

Follow up on the latest improvements and updates.

RSS

new

improved

fixed

ATCC uploads and sample-appropriate analyses

Fixed
  • The upload panel for ATCC Discrepancy Reports has been fixed to now allow upload of interleaved or single-end files.
Changed
  • The Targeted Loci Database can no longer be run on samples sequenced by One Codex, as these are not generated using an amplicon library preparation approach.

new

improved

fixed

One Codex Python Library updated to 0.17.0

The onecodex python library and CLI has been updated with the following changes.
Added
  • Adds
    SampleCollection.beta_diversity_stats()
    to test for significant differences between groups of samples based on their beta diversity distances (global and posthoc pairwise PERMANOVA tests are supported)
  • Adds categorical data palette to
    onecodex
    Altair theme
  • Adds support for passing both
    facet_by
    and
    secondary_haxis
    to
    plot_metadata()
  • Adds filtering and warning if samples are missing abundances in
    plot_metadata()
    ,
    plot_pcoa()
    ,
    plot_mds()
    ,
    plot_pca()
    ,
    alpha_diversity_stats()
    , and
    beta_diversity_stats()
  • Adds docs about Shannon diversity being calculated using log base 2 instead of base
    e
Changed
  • Upgrades Altair to 5.4.1 and replaces
    altair_saver
    with
    vl-convert
  • Upgrades
    notebook
    to 6.5.7
  • Upgrades
    WeasyPrint
    to 63.0
  • Removes
    node
    and
    vega
    npm dependencies
  • Removes
    jupyter-client
    dependency
  • Removes
    selenium
    dependency
  • Removes pinned
    pydyf
    version
Fixed
  • Fixes
    Api()
    call when Altair is not installed
  • Fixes scikit-bio and pandas warnings
  • Improves error message and docstring in
    SampleCollection.to_df(normalize=False)
Deprecated
  • Deprecates
    AlphaDiversityStatsResults.posthoc_df
    in favor of
    AlphaDiversityStatsResults.posthoc.adjusted_pvalues
More details are available in GitHub.

improved

fixed

Minor Custom Plots Updates

New
  • "Facet By" and "Secondary Group By" can now be used together in alpha diversity plots. In previous versions, these two plotting parameters were exclusive.
Fixed
  • You can now edit multiple titles on plots (e.g. plot title, legend title, x-axis or y-axis labels). We have addressed a bug that prevented editing other titles/fields after one has been edited.

new

Workflows can now depend on other workflows

We've just added a new feature to Workflows: Dependencies! Dependencies are workflows that are required by other workflows. When creating a workflow, "workflow C" (child), if you need the outputs from another workflow, "workflow P" (parent), to be available as inputs, you can set "workflow P" (parent) as a Dependency for "workflow C" (child). Here are some of the details to know:
  • Running a workflow that has dependencies will automatically launch the dependency workflows on the sample, with default arguments, unless that workflow has already been run.
  • All output files from from a parent workflow will be available in the specified directory of a child workflow.
  • If a parent workflow has been run previously, the most recently-run version will be used as the dependency, regardless of the arguments used.
  • You can only publish a workflow if all of its dependencies have also been published.
  • If you run workflows and dependencies in a draft state, and then publish the workflows, running the child workflow will rerun the newly-published parent workflows. We will not use draft runs as inputs to published workflow runs.
  • If running a child workflow, and a parent workflow fails, the child will be marked as failed, until the parent workflow completed successfully.
  • Rerunning a failed parent workflow will also rerun any child workflows that depend on it.

fixed

Fixed string to boolean discrepancy in workflow arguments

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

Download subset of reads through browser

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

Element Aviti sequencers detected

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

Fixes for Jobs.get through experimental library and files with leading `.`

Fixed
  • Workflow output files beginning with
    .
    will no longer be stripped of their
    .
    . Only files with
    ./
    will be stripped of the
    ./
    . (Example,
    .nextflow.log
    will no longer be stripped of the leading
    .
    ).
  • ocx.Jobs.get
    now works in the experimental onecodex API

new

2024 One Codex Database Released

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

fixed

new

New File details endpoint, and display fixes

New
  • Added
    file_details
    API 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.gz
    extensions 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.
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