2023.03

• Added "Sample Validation" for all Admin levels.
• Tools and Plugins can add preparation information via the endpoint: /qiita_db/prep_template/.
• Users can now access specific preparations via the URL by adding it as a parameter: /study/description/<study_id>?prep_id=<prep_id>.
• The internal Sequence Processing Pipeline now automatically inserts new BLANKs to the sample information file, adds the preparation information file to Qiita, and keeps a record of which preparations were inserted to which studies.
• Added the possibility of processing BIOM artifacts in the processing pipeline.
• Added qiime2.2023.2 to the system; which updated these plugins: qp-qiime2, qtp-biom, qtp-diversity, qtp-visualization.
• Added q2-greengeenes2 to the system, specifically actions: filter_features and non_v4_16s. This is the first processing (vs. analysis) plugin added to the system.
• Fixed the diversity pcoa_biplot functionality and added the emperor biplot action.
• The system can now validate QIIME 2 FeatureData[Sequences] via qtp-diversity.
• Fixed the following issues: #3249, #3264, #3245, #3243.

2023.02

• Added "Software and Data Licensing" to the Qiita FAQ page.
• External resources can now add new sample metadata categories to a study via
  the /api/v1/study/ endpoint.
• Added preparation-id to the GUI list of artifacts used in an analysis.
• Added automatic lower-casing to INSDC null values #3246.
• ArtifactHandler now returns the file size and full path of the files available in
  an Artifact. This change had two consequences: (1) the plugins now can control
  their behavior based on the file sizes, and (2) all plugins had to be updated to use this new feature.
• Added qiita_client.artifact_and_preparation_files
  to help plugins filter per_sample_FASTQ based on size and ignore small file sizes.
• Added qiime2.2022.11 to the system; which updated these plugins: qp-qiime2, qtp-biom, qtp-diversity, qtp-visualization.
• Added q2-mislabeled and composition's ancom to the qiime2.2022.11 deployment.
• Added support for Amplicon data to the internal Sequence Processing Pipeline.

2022.11

• Adding new Woltka v0.1.4 and WoLr2 - WoLr1 and RS210 (updated version of rep200) are available but not default.
• Update qp-woltka so it runs faster, contribution with @wasade. Add newest improvements for woltka processing so it runs faster.
• Fix qp-qiime2, "filter features" bug that expects a "feature metadata" value from the dropdown.
• Avoid having multiple git version commands running in the system - this in theory should fix some of the slow downs.
• Fix sample_name in per preparation sample information files.
• Now the sequencing artifacts (like per-sample-FASTQ, FASTA, etc) accept log files.
• SortMeRNA via qp-meta will generate processing logs and will be added to their artifacts - note that this will only be available in newer runs AKA you can delete the outputs of past runs and rerun it.
• Added new "Admin Sample Validation" to validate a list of sample names against what's available in a study, contributed by @sarayupai.

2022.09

• Moved Qiita's code base and plugins to SLURM (from Torque). The plugins updated are: qiita-spots/qp-woltka, biocore/mg-scripts, qiita-spots/qp-spades, qiita-spots/qp-meta, qiita-spots/qp-fastp-minimap2.
• Pinned the paramiko version to < 2.9 as newer versions were causing issues with older systems.
• Pinned the scipy version to < 1.8 to avoid issues with the biom-format library.
• Updates to the INSTALL instructions (thank you @aliu104 !)

2022.07

• Users can opt-in to get emails when their jobs change status in their User Information preferences.
• Added BIOM artifact archiving to the system; this unlinks artifacts from the main processing but leaves them in the system in case they are needed in the future.
• Added qiime2.2022.02 to the system; which updated these plugins: qp-qiime2, qtp-biom, qtp-diversity, qtp-visualization
• Users can now select multiple artifacts for analysis qp-qiime2, which gives access to new commands like PCoA biplots.
• qtp-sequencing now uses fqtools to count the number of sequences in fastq/fastq.gz files as part as the artifact summary.
• Artifact summaries can now be updated qiita-spots #3205.
• Added to the internal Sequence Processing Pipeline the CHM13 genome so human studies are now filtered by GRCh38 genome + PhiX and CHM13 genome.

2022.05

• Added Artifact.iter() for easier Artifact interactions.
• Fixed the SCP Qiita transfer; this was the problem and solution.
• Added User.email to the Admin Job Processing listing.

2022.04

• Moved from Python 3.6 to 3.9.
• Added support for Pandas 1.4.0, details here.
• Updated all available JavaScript libraries, details here.
• Users can select which metadata to use when creating a new analysis. By default only overlapping metadata in all studies is selected.
• Now we can fully delete users in the backend.
• Updated documentation to reflect the new EMPO version 2.
• Fixed outstanding issues to add default workflow to a preparation, details here.
• Fixed the following issues: 3183, 3182, 3170, 3193.
• We deprecated the use of specimen_id from Qiita; this is no longer required in the backend or the GUI.
• Moved qp-fastp-minimap2 to per sample parallelization. Now an iSeq processing takes ~20min, while before it took close to 2hrs.
• Fixed the following issues qp-knight-lab-processing #15, qp-knight-lab-processing #16, qp-knight-lab-processing #17, qp-knight-lab-processing #19, mg-scripts #60, mg-scripts #62 from the Knight Lab Sequence Processing Pipeline.

2021.11

• Upgrading PostgreSQL from 9.5 to 13.4 as 9.5 is no longer supported
• Updated SortMeRNA within qt-meta to filter RNA reads to run as job arrays to speed up processing. A full NovaSeq run will now take ~15hrs vs. ~161hrs.
• Added qiime2.2021.11 to the system; which updated these plugins: qp-qiime2, qtp-biom, qtp-diversity, qtp-visualization.
• Jobs no longer need to be linked to studies or analyses; this allows us to create general purpose jobs like "admin like" jobs that can be fully traced in Qiita.
• Added a new user level: "wet-lab admin" so they can start "admin like" jobs in the system without having to be an actual admin.
• Added a new plugin: "qp-knight-lab-processing" that provides the general Knight Lab sequence processing: from BCL to per_sample_FASTQ to the upload folders in Qiita.
• Added "Oxford_Nanopore" as a valid "platform" with "GridION" as valid "instrument_model" to the system; this allows submission of this data to EBI-ENA.
• Allow chucked download of metadata files in analyses; this allows to process large meta-analysis (like those for The Microsetta Initiative) without worker blockage.
• Added to the qp-qiime2 plugin the possibility of filtering tables based on system available "FeatureData[Sequence]"; to start we added 90/100/150 bps bloom tables.
• Now we can instantiate a study via their title (Study.from_title); this will facilitate orchestration with qebil.
• Speed up Study listing for admins and general users; the admin study display came down from 20 to 2 seconds.
• Fixed the following issues: 3142, 3149, 3150, 3119, and 3160.

2021.09

• Updated the qp-deblur plugin to version 2021.09 addressing a bug in fragment insertion parsing and caching; more information.
• Double the number of possible connections for the Qiita database: 100 -> 200 simultaneous connections.
• Added a new data type: "Job Output Folder" and artifact type definition: "job-output-folder" to initially support admin-only standalone commands in Qiita.
• The study listing is now sorted by descending study id and then ascending number of available artifacts.
• Removed old code from the Sample Information update method that regenerated all preparations in that study - this is no longer necessary as the per preparation sample information files are built on the fly.
• Fixed a bug that did not copy the raw files when adding a new artifact via the CLI.
• Fixed the following issues: #3124, #3122, #3134.

2021.07

• Added a new "Add Default Workflow" button to the preparation tab so we automatically add all the "recommended" steps in a preparation based on our workflows.
• New Preparation Listing GUI + searching within preparation types, thank you @AmandaBirmingham!
• We limit the parameters displayed to the user per command based on which have already been run successfully; for example if a preparation has already a "Trim 100" job, this option will not be shown.
• Re-added Coveralls to Qiita and removed codecov.
• We are limiting the number of samples in a preparation file to 800.
• Added User.update_email which allows to update a Users email.
• Fixed the following issues: #3113, and #3079.