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qiime2-amplicon-2023.9 #82

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6 changes: 3 additions & 3 deletions .github/workflows/qiita-plugin-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -77,9 +77,9 @@ jobs:
- name: Install Qiita plugins
shell: bash -l {0}
run: |
wget --quiet https://data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.yml
conda env create -n qiime2 --quiet --file qiime2-2023.5-py38-linux-conda.yml
rm qiime2-2023.5-py38-linux-conda.yml
wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2023.9-py38-linux-conda.yml
conda env create -n qiime2 --file qiime2-amplicon-2023.9-py38-linux-conda.yml
rm qiime2-amplicon-2023.9-py38-linux-conda.yml

conda activate qiime2

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4 changes: 2 additions & 2 deletions qp_qiime2/__init__.py
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Expand Up @@ -60,13 +60,13 @@
qiita_artifact = 'BIOM'

if q2plugin.name not in Q2_ANALYSIS_PLUGINS:
# As of qiime2-2022.11 this filters out:
# As of qiime2-2023.9 this filters out:
# alignment
# deblur
# diversity-lib
# feature-classifier
# fragment-insertion
# greengenes2
# greengenes2 - added as processing plugin
# quality-control
# sourcetracker2
# vsearch
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2 changes: 1 addition & 1 deletion qp_qiime2/qp_qiime2.py
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Expand Up @@ -25,7 +25,7 @@

Q2_ANALYSIS_PLUGINS = [
'taxa', 'sample-classifier', 'composition', 'phylogeny', 'feature-table',
'gneiss', 'diversity', 'longitudinal', 'emperor', 'umap', 'mislabeled'
'diversity', 'longitudinal', 'emperor', 'umap', 'mislabeled'
]

Q2_PROCESSING_PLUGINS = [
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65 changes: 30 additions & 35 deletions qp_qiime2/util.py
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Expand Up @@ -119,15 +119,14 @@ def register_qiime2_commands(plugin, methods_to_add, q2_expected_plugins,
qt_name, predicate = get_qiime2_type_name_and_predicate(element)

if qt_name not in Q2_QIITA_SEMANTIC_TYPE:
# As of qiime2-2022.2 this filters out:
# Hierarchy
# gneiss dendrogram_heatmap
# gneiss ilr_hierarchical
# SampleEstimator
# sample-classifier predict_classification
# sample-classifier predict_regression
# As of qiime2-2023.9 this filters out:
# Collection
# feature-table tabulate_seqs taxonomy
# ProcrustesStatistics
# emperor procrustes_plot
# emperor procrustes_plot m2_stats
# SampleEstimator
# sample-classifier predict_classification sample_estimator
# sample-classifier predict_regression sample_estimator
add_method = False
break

Expand All @@ -150,14 +149,15 @@ def register_qiime2_commands(plugin, methods_to_add, q2_expected_plugins,
req_params[element.description] = ('artifact', ['BIOM'])
to_delete.append(pname)
else:
# As of qiime2-2022.2 this filters out:
# predicate: Importance
# importance heatmap
# importances plot_feature_volatility
# predicate: Differential
# differential ilr_phylogenetic_differential
# As of qiime2-2023.9 this filters out:
# predicate: AlignedSequence | Sequence
# data tabulate_seqs
# feature-table tabulate_seqs
# predicate: DifferentialAbundance
# composition da_barplot
# composition tabulate
# predicate: Importance
# longitudinal plot_feature_volatility
# sample-classifier heatmap
add_method = False
elif etype == 'TaxonomicClassifier':
default = qp_qiime2_dbs[0]
Expand Down Expand Up @@ -190,28 +190,23 @@ def register_qiime2_commands(plugin, methods_to_add, q2_expected_plugins,
element)
if (qt_name not in Q2_QIITA_SEMANTIC_TYPE or
qt_name in NOT_VALID_OUTPUTS):
# As of qiime2-2022.2 this filters out:
# Hierarchy
# gneiss assign_ids
# gneiss correlation_clustering
# gneiss gradient_clustering
# gneiss ilr_phylogenetic
# As of qiime2-2023.9 this filters out:
# Collection
# feature-table split tables
# Phylogeny
# gneiss ilr_phylogenetic_differential
# gneiss ilr_phylogenetic_ordination
# phylogeny align_to_tree_mafft_fasttree
# phylogeny align_to_tree_mafft_iqtree
# phylogeny align_to_tree_mafft_raxml
# phylogeny filter_tree
# SampleEstimator
# longitudinal feature_volatility
# longitudinal maturity_index
# sample-classifier classify_samples
# sample-classifier fit_classifier
# sample-classifier fit_regressor
# sample-classifier regress_samples
# phylogeny align_to_tree_mafft_fasttree tree
# phylogeny align_to_tree_mafft_iqtree tree
# phylogeny align_to_tree_mafft_raxml tree
# phylogeny filter_tree tree
# ProcrustesStatistics
# diversity procrustes_analysis
# diversity procrustes_analysis disparity_results
# SampleEstimator
# longitudinal feature_volatility sample_estimator
# longitudinal maturity_index sample_estimator
# sample-classifier classify_samples sample_estimator
# sample-classifier fit_classifier sample_estimator
# sample-classifier fit_regressor sample_estimator
# sample-classifier regress_samples sample_estimator
add_method = False
break
else:
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