Doc improvements (#3437)

* doc improvemnts

* doc improvements

* METAGENOMICS -> Metagenomics

* 2024.10

* scp -O

.github/workflows/qiita-ci.yml

@@ -179,7 +179,7 @@ jobs:
           echo "Connecting as $USER@localhost"
           # this line (and the -o StrictHostKeyChecking=no) is so the server
           # is added to the list of known servers
-          scp -o StrictHostKeyChecking=no -i $PWD/qiita_ware/test/test_data/test_key $USER@localhost:/home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key /home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key_copy_1
+          scp -O -o StrictHostKeyChecking=no -i $PWD/qiita_ware/test/test_data/test_key $USER@localhost:/home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key /home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key_copy_1
 
       - name: Main tests
         shell: bash -l {0}

CHANGELOG.md

@@ -1,17 +1,19 @@
 # Qiita changelog
 
-Version 2024.09
+Version 2024.10
 ---------------
 
-Deployed on September 23rd, 2024
+Deployed on October 14th, 2024
 
 * Added update_resource_allocation_redis and companion code, so resource allocations summaries are available for review. Thank you @Gossty!
 * Now is possible to have default workflows with only one step.
 * `qiita_client.update_job_step` now accepts an ignore_error optional parameter. Thank you @charles-cowart!
 * Initial changes in `qiita_client` to have more accurate variable names: `QIITA_SERVER_CERT` -> `QIITA_ROOTCA_CERT`. Thank you @charles-cowart!
 * Added `get_artifact_html_summary` to `qiita_client` to retrieve the summary file of an artifact.
 * Re-added github actions to `https://github.com/qiita-spots/qiita_client`.
-* `Woltka v0.1.6, paired-end` superseded `Woltka v0.1.6` in `qp-woltka`; [more information](https://qiita.ucsd.edu/static/doc/html/processingdata/woltka_pairedend.html). Thank you to @qiyunzhu for the benchmarks!
+* `SortMeRNA v4.3.7` superseded `Sortmerna v2.1b`, which relies on Silva 138 and now produced even mates. Thank you @ekopylova and @biocodz for the support.
+* `Remove SynDNA reads` superseded `SynDNA Woltka`, which now generates even mates.
+* `Woltka v0.1.7, paired-end` superseded `Woltka v0.1.6` in `qp-woltka`; [more information](https://qiita.ucsd.edu/static/doc/html/processingdata/woltka_pairedend.html). Thank you to @qiyunzhu for the benchmarks!
 * Other general fixes, like [#3424](https://github.com/qiita-spots/qiita/pull/3424), [#3425](https://github.com/qiita-spots/qiita/pull/3425).
 
 

qiita_core/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2024.09"
+__version__ = "2024.10"

qiita_db/__init__.py

@@ -27,7 +27,7 @@
 from . import user
 from . import processing_job
 
-__version__ = "2024.09"
+__version__ = "2024.10"
 
 __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__ = "2024.09"
+__version__ = "2024.10"

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__ = "2024.09"
+__version__ = "2024.10"
 
 __all__ = ['prep_template_summary_get_req', 'data_types_get_req',
            'study_get_req', 'sample_template_filepaths_get_req',

qiita_pet/support_files/doc/source/faq.rst

@@ -414,13 +414,18 @@ Are you planning a workshop or class?
 -------------------------------------------------------------------
 
 We encourage users to use Qiita for their classes and/or workshops and to facilitate processing
-we urge  users to request a special reservation in the system. A reservation should help your
+we urge them to request a special reservation in the system. A reservation should help your
 and your participant jobs to move quicker in the system. If you are interested, please send us
 an email to qiita.help@gmail.com and add the name of your workshop/course, the number of
 participants, the expected days this will happen. Note that reservations are only available for
 analysis and not for sequencing processing, and that the reservation can be added/edited during
 the creation of the analysis or at any point within each individual analysis page.
 
+You can add the reservation string to the analysis at the time of creation (bottom of the creation
+page), or the analysis page via the reservation button (top right). Note that once the reservation
+time finishes, your jobs will fail as the reservation will no longer exist so you will need to
+remove it - we suggest doing this before submitting new jobs.
+
 How to cite Qiita?
 ------------------
 

qiita_ware/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2024.09"
+__version__ = "2024.10"

qiita_ware/ebi.py

@@ -110,6 +110,7 @@ class EBISubmission(object):
                                     'ILLUMINA MISEQ',
                                     'ILLUMINA MINISEQ',
                                     'ILLUMINA NOVASEQ 6000',
+                                    'ILLUMINA NOVASEQ X',
                                     'NEXTSEQ 500',
                                     'NEXTSEQ 550',
                                     'UNSPECIFIED'],
@@ -539,7 +540,7 @@ def generate_experiment_xml(self, samples=None):
             library_name.text = self._get_library_name(sample_name)
 
             lg = ET.SubElement(library_descriptor, 'LIBRARY_STRATEGY')
-            lg.text = escape(clean_whitespace(library_strategy.upper()))
+            lg.text = escape(clean_whitespace(library_strategy))
 
             # hardcoding some values,
             # see https://github.com/biocore/qiita/issues/1485

qiita_ware/test/test_ebi.py

@@ -1358,7 +1358,7 @@ def test_parse_EBI_reply(self):
 %(study_id)s.Sample1" />
       <LIBRARY_DESCRIPTOR>
         <LIBRARY_NAME>%(study_id)s.Sample1</LIBRARY_NAME>
-        <LIBRARY_STRATEGY>METAGENOMICS</LIBRARY_STRATEGY>
+        <LIBRARY_STRATEGY>Metagenomics</LIBRARY_STRATEGY>
         <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
         <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
         <LIBRARY_LAYOUT><SINGLE /></LIBRARY_LAYOUT>
@@ -1393,7 +1393,7 @@ def test_parse_EBI_reply(self):
 %(study_id)s.Sample2" />
       <LIBRARY_DESCRIPTOR>
         <LIBRARY_NAME>%(study_id)s.Sample2</LIBRARY_NAME>
-        <LIBRARY_STRATEGY>METAGENOMICS</LIBRARY_STRATEGY>
+        <LIBRARY_STRATEGY>Metagenomics</LIBRARY_STRATEGY>
         <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
         <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
         <LIBRARY_LAYOUT><SINGLE /></LIBRARY_LAYOUT>
@@ -1428,7 +1428,7 @@ def test_parse_EBI_reply(self):
 %(study_id)s.Sample3" />
       <LIBRARY_DESCRIPTOR>
         <LIBRARY_NAME>%(study_id)s.Sample3</LIBRARY_NAME>
-        <LIBRARY_STRATEGY>METAGENOMICS</LIBRARY_STRATEGY>
+        <LIBRARY_STRATEGY>Metagenomics</LIBRARY_STRATEGY>
         <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
         <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
         <LIBRARY_LAYOUT><SINGLE /></LIBRARY_LAYOUT>
@@ -1469,7 +1469,7 @@ def test_parse_EBI_reply(self):
       <SAMPLE_DESCRIPTOR accession="ERS000008" />
       <LIBRARY_DESCRIPTOR>
         <LIBRARY_NAME>1.SKB2.640194</LIBRARY_NAME>
-        <LIBRARY_STRATEGY>METAGENOMICS</LIBRARY_STRATEGY>
+        <LIBRARY_STRATEGY>Metagenomics</LIBRARY_STRATEGY>
         <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
         <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
         <LIBRARY_LAYOUT><SINGLE /></LIBRARY_LAYOUT>
@@ -1558,7 +1558,7 @@ def test_parse_EBI_reply(self):
       <SAMPLE_DESCRIPTOR accession="ERS000024" />
       <LIBRARY_DESCRIPTOR>
         <LIBRARY_NAME>1.SKB3.640195</LIBRARY_NAME>
-        <LIBRARY_STRATEGY>METAGENOMICS</LIBRARY_STRATEGY>
+        <LIBRARY_STRATEGY>Metagenomics</LIBRARY_STRATEGY>
         <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
         <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
         <LIBRARY_LAYOUT><SINGLE /></LIBRARY_LAYOUT>

setup.py

@@ -10,7 +10,7 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "2024.09"
+__version__ = "2024.10"
 
 
 classes = """