QIIME 2 2020.8 is now available!

Announcements
1

The QIIME 2 2020.8 release is now available! Thanks to everyone involved for their hard work!

As a reminder, our next planned QIIME 2 release is scheduled for November 2020 (QIIME 2 2020.11), but please stay tuned for updates.

Check out the QIIME 2 2020.8 docs for details on installing the latest QIIME 2 release, as well as tutorials and other resources. Get in touch on the QIIME 2 Forum if you run into any issues!

Virtual machine builds will be available sometime within the next week - watch this topic thread for an update!

:exclamation: BREAKING CHANGES

  • q2-diversity
    • beta-phylogenetic
      • The parameter threads has replaced n_jobs to reflect the parallelization behavior of unifrac.
    • alpha
      • The metric name observed_otus has been renamed to observed_features. “Observed features” better describes the different ways in which users work with non-taxonomic features in QIIME 2. (An OTU is a feature, but a feature isn’t necessarily an OTU.)
      • This Method has been converted to a Pipeline to accommodate dispatch to q2_diversity_lib. Artifact API users might need to update their import paths. q2cli users are not impacted by this change.
    • alpha-phylogenetic
      • This Method has been converted to a Pipeline to accommodate dispatch to q2_diversity_lib. Artifact API users might need to update their import paths. q2cli users are not impacted by this change.
    • alpha-rarefaction
      • The metric name observed_otus has been renamed to observed_features. “Observed features” better describes the different ways in which users work with non-taxonomic features in QIIME 2. (An OTU is a feature, but a feature isn’t necessarily an OTU.)
    • beta
      • This Method has been converted to a Pipeline to accommodate dispatch to q2_diversity_lib. Artifact API users might need to update their import paths. q2cli users are not impacted by this change.
      • The wminkowski and mahalonobis metrics were buggy, and have been removed from the list of available metrics. They will be reimplemented in future.
    • beta-phylogenetic
      • This Method has been converted to a Pipeline to accommodate dispatch to q2_diversity_lib. Artifact API users might need to update their import paths. q2cli users are not impacted by this change.
    • alpha-phylogenetic-old
    • alpha-phylogenetic-alt
      • This deprecated Method has been removed, because this implementation is used in alpha-phylogenetic.
  • q2-quality-filter
    • q-score-joined
      • This deprecated method was removed. The q-score method can handle joined reads, so no need to for two methods.

Please update scripts, workflows, etc. as appropriate. Stuck? Reach out here on the forum for help. Want to test this prior to the next release of QIIME 2? Check on the “development environment” instructions here:

https://dev.qiime2.org/latest/quickstart/

Here’s the highlights of the release:

  • QIIME 2 Framework

    • @Oddant1 fixed a bug preventing the usage of TypeMatch on Actions with a List or Set type parameter. :balance_scale:
    • @Oddant1 changed an error message so it points out a common mistake seen when importing metadata. :t_rex:
    • @Oddant1 fixed the error message reporting duplicated transformers, which can happen when developing a QIIME 2 plugin. :balloon:

  • docs

    • @Oddant1 changed all references to the deprecated q-score-joined method to q-score. Please see BREAKING CHANGES, above. :bike:
    • @andrewsanchez provided some editorial services for a few tutorials! :unicorn:

  • q2-types

    • @Oddant1 implemented improved validation for AlignedDNAFASTAFormat. :safety_vest:
    • @Oddant1 added an extra check during the creation of MANIFEST files for CasavaOneEightSingleLanePerSampleDirFmt to better allow for reverse only reads. :lacrosse:
    • New types and formats were added for working with Bowtie2 index files. :bow_and_arrow:
    • @Leo-Simpson (GH) added a new FeatureTable variant, called Design. It represents transformed/coded data, as an alternative to composition which only positive values. :desert_island:

  • q2-phylogeny

    • @SoilRotifer updated the citation for IQ-TREE 2. :nail_care:
    • @SoilRotifer added a new n_cores_auto parameter to iqtree and iqtree-ultrafast-bootstrap, used when n_cores auto is set. That is, n_cores_max will limit how many cores auto is allowed to scale to. :oden:

  • q2-longitudinal

  • q2-sample-classifier

    • @Oddant1 cleaned up new linting errors introduced by the latest flake8. :city_sunset:
    • @Leo-Simpson (GH) added support for the new FeatureTable[Design] type in split-table. :non-potable_water:

  • q2-quality-filter

    • @Oddant1 removed the previously deprecated q_score_joined Method. Please see BREAKING CHANGES, above. :baby_chick:

  • q2-diversity

    • @Oddant1 fixed a bug in alpha_rarefaction that prevented metadata with a column named “depth” from working as expected. :bug:
    • @ChrisKeefe wired up alpha, alpha_phylogenetic, beta, beta_phylogenetic, and alpha_rarefaction to metrics implemented in q2_diversity_lib, for improved type flexibility, safety, and specificity in primary source citations. See BREAKING CHANGES above for related API changes. :electric_plug:

  • q2-diversity-lib

    • @ChrisKeefe added alpha_passthrough, beta_passthrough, and beta_phylogenetic_passthrough Methods, which provide access to unifrac and scikit-bio metrics that have not yet been implemented/constrained locally. Most users will prefer to access these Methods indirectly, using diversity.alpha, diversity.beta, or diversity.beta_phylogenetic :crystal_ball:

  • q2-demux

    • @Oddant1 modified demux summarize to better support reverse only reads. :previous_track_button:

  • q2-dada2

    Happy QIIMEing! :fallen_leaf:

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Yippee! Freshly baked VMs were just pulled out of the oven:

:bread: :croissant: :pie:

https://docs.qiime2.org/2020.8/install/virtual/

Enjoy!

:qiime2:

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Thanks for the update! Unfortunately, there seems to be something wrong with the version in the .zip folder. The .zip itself states 2020.8 but inside the folder, .ovf file and disk image all state 2020.6.
I installed it anyway to check, its indeed 2020.6.

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Thanks @robdalen - this was caused by human error on my part. I am rebuilding now, hopefully should have that up in the next few hours. Will update here when its been replaced. Thanks!

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@robdalen - I just pushed up what I think is the right vbox build (Build ID 1598972704). Please give that a shot, thanks!

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@thermokarst Works like a charm, thanks!

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