Merge f935a3e into ec231d5

Author: antgonza

CHANGELOG.md

@@ -1,5 +1,28 @@
 # Qiita changelog
 
+Version 2025.11
+---------------
+
+Deployed on Novermber 25th, 2025
+
+* Updated `qp-knight-lab-processing` to add support of PacBio raw data processing that has twisted adaptors, including human-filtering using MOVI. Also, replaced flake8 for ruff. Additionally, added `IsPairedEndComplete` as part of the Illumina xml validation process.
+* Added a new plugin to the system: `https://github.com/qiita-spots/qp-pacbio`, which adds two new commands: `Woltka v0.1.7, minimap2` and `PacBio processing`.
+* Added default workflows specific to PacBio.
+* Allowed default workflows to have multiple commands starting from a single input. 
+* Now users can download public raw and biom per-preparation directly.
+* Initial changes for to support cloud environments via cloud specific endpoints; thank you @sjanssen2!
+
+
+Version 2025.09
+---------------
+
+Deployed on September 11th, 2025
+
+* Updated `qp-knight-lab-processing` to add support of PacBio raw data processing, including human-filtering using MOVI.
+* Updated fastp in local environment for `qp-knight-lab-processing` from 0.20.1 to 0.23.4.
+* Added workflows parameters to the default workfows in Qiita to make them Illumina specific: `UPDATE qiita.default_workflow set parameters = '{"prep": {"platform": "Illumina"}, "sample": {}}'::json WHERE default_workflow_id IN (4, 6, 9 ,11);` to avoid PacBio processing applying them.
+
+
 Version 2025.07
 ---------------
 

qiita_core/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2025.07"
+__version__ = "2025.11"

qiita_db/__init__.py

@@ -27,7 +27,7 @@
 from . import user
 from . import processing_job
 
-__version__ = "2025.07"
+__version__ = "2025.11"
 
 __all__ = ["analysis", "artifact",  "archive", "base", "commands",
            "environment_manager", "exceptions", "investigation", "logger",

qiita_pet/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2025.07"
+__version__ = "2025.11"

qiita_pet/handlers/api_proxy/__init__.py

@@ -38,7 +38,7 @@
 from .user import (user_jobs_get_req)
 from .util import check_access, check_fp
 
-__version__ = "2025.07"
+__version__ = "2025.11"
 
 __all__ = ['prep_template_summary_get_req', 'data_types_get_req',
            'study_get_req', 'sample_template_filepaths_get_req',

qiita_pet/support_files/doc/source/downloading.rst

@@ -87,6 +87,7 @@ replace artifact-id):
 
 - https://qiita.ucsd.edu/public_artifact_download/?artifact_id=artifact-id
 
+
 Access non-public artifacts without a login
 -------------------------------------------
 
@@ -115,7 +116,9 @@ can be used to download BIOMs or raw data. Do not forget to replace `study-id`,
 - Only 16S raw data: https://qiita.ucsd.edu/public_download/?data=raw&study_id=study-id&data_type=16S
 - Only Metagenomic BIOMs + mapping files: https://qiita.ucsd.edu/public_download/?data=biom&study_id=study-id&data_type=Metagenomic
 - Only the sample information file: https://qiita.ucsd.edu/public_download/?data=sample_information&study_id=study-id
-- Only the preparation information file: https://qiita.ucsd.edu/public_download/?data=data=prep_information&prep_id=prep-id
+- Only the preparation information file: https://qiita.ucsd.edu/public_download/?data=prep_information&prep_id=prep-id
+- Raw data for a given preparation: https://qiita.ucsd.edu/public_download/?data=raw&prep_id=prep-id
+- BIOM data for a given preparation: https://qiita.ucsd.edu/public_download/?data=biom&prep_id=prep-id
 
 Note that if you are downloading raw data, the owner should have made that data
 available by selecting "Allow Qiita users to download raw data files" in

qiita_ware/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2025.07"
+__version__ = "2025.11"

setup.py

@@ -10,7 +10,7 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "2025.07"
+__version__ = "2025.11"
 
 
 classes = """