Feat sklearn pca50 by tonyliang19 · Pull Request #114 · CompBio-Lab/MESSI-pipeline

tonyliang19 · 2026-09-29T14:20:19Z

No description provided.

Major change to prepare data, seed reproduce

feat: add the final samplesheet used for the pipeline

…temp var option

…cli and config

Copilot

Copilot review overview

🔵 Needs a closer look

Unresolved feature-selection and container issues affect execution, and the broad workflow changes need final human review.

Review effort: Balanced
Findings: 3 · 1

Open (4)

MLP default breaks sklearn feature selection · New
Sklearn tasks use the wrong container image · New
Removed SGMR include leaves an undefined workflow call · New
Event column option is ignored by the workflow · New

What changed in this PR

This PR adds per-modality PCA-50 to sklearn training in the multi-omics pipeline. It also changes splitting, container configuration, and the set of available workflows.

Changes:

Add sklearn reduction options, classifiers, and feature-selection search changes.
Add survival-event splitting and revise classification metrics.
Centralize process containers and remove simulation and placeholder methods.

File	Description
`subworkflows/splitting/main.nf`	Passes outcome type to splitting.
`subworkflows/simulation/main.nf`	Removes simulation workflow.
`subworkflows/prepare_data/main.nf`	Removes simulation include.
`subworkflows/methods/sklearn/main.nf`	Passes reduction options to training.
`subworkflows/methods/sgmr/main.nf`	Removes SGMR placeholder.
`subworkflows/cross_validation/r/main.nf`	Removes SGMR include.
`subworkflows/cross_validation/python/main.nf`	Removes GOAT integration.
`subworkflows/cross_validation/main.nf`	Updates Python-method run condition.
`nextflow.config`	Sets defaults and container labels.
`modules/split_train_test/resources/usr/bin/split_tr_te.py`	Adds survival-event splitting.
`modules/split_train_test/main.nf`	Forwards outcome type.
`modules/sklearn/train/resources/usr/bin/sklearn_train.py`	Adds modality-wise PCA pipeline.
`modules/sklearn/train/resources/usr/bin/load_classifier_class.py`	Revises classifier choices.
`modules/sklearn/train/resources/usr/bin/combine_mdata2df.py`	Returns modality names.
`modules/sklearn/train/main.nf`	Runs training by model and reduction.
`modules/sklearn/select_feature/resources/usr/bin/sklearn_select_features.py`	Flattens feature-selection targets.
`modules/sklearn/select_feature/resources/usr/bin/run_random_search_cv.py`	Searches parameters in a scaling pipeline.
`modules/sklearn/select_feature/resources/usr/bin/load_classifier_class.py`	Revises selection classifiers.
`modules/sklearn/select_feature/main.nf`	Uses a container label.
`modules/sklearn/preprocess/main.nf`	Uses a container label.
`modules/sklearn/predict/main.nf`	Uses a container label.
`modules/simulation/simulate_mvn_data/resources/usr/bin/unique_matrices.R`	Removes simulation helper.
`modules/simulation/simulate_mvn_data/resources/usr/bin/simulate_data.R`	Removes simulation script.
`modules/simulation/simulate_mvn_data/resources/usr/bin/gen_simul_metadata.R`	Removes metadata generator.
`modules/simulation/simulate_mvn_data/resources/usr/bin/debug_simulate_data.R`	Removes simulation debug script.
`modules/simulation/simulate_mvn_data/main.nf`	Removes MVN simulation process.
`modules/simulation/simulate_intersim/resources/usr/bin/simulate_InterSIM.R`	Removes InterSIM script.
`modules/simulation/simulate_intersim/resources/usr/bin/save_mudata.py`	Removes simulation export helper.
`modules/simulation/simulate_intersim/main.nf`	Removes InterSIM process.
`modules/rgcca/train/main.nf`	Uses an RGCCA container label.
`modules/rgcca/select_feature/main.nf`	Uses an RGCCA container label.
`modules/rgcca/preprocess/main.nf`	Uses an RGCCA container label.
`modules/rgcca/predict/main.nf`	Uses an RGCCA container label.
`modules/prepare_data/uncompress_record/main.nf`	Uses a generic container label.
`modules/prepare_data/prepare_mu_data/main.nf`	Uses a generic container label.
`modules/prepare_data/prepare_mae_data/main.nf`	Uses a generic container label.
`modules/prepare_data/parse_metadata/main.nf`	Uses a generic container label.
`modules/mogonet/train/main.nf`	Uses a MOGONET container label.
`modules/mogonet/select_feature/main.nf`	Uses a MOGONET container label.
`modules/mogonet/preprocess/main.nf`	Uses a MOGONET container label.
`modules/mogonet/predict/main.nf`	Uses a MOGONET container label.
`modules/mofa/train/main.nf`	Uses a MOFA container label.
`modules/mofa/select_feature/main.nf`	Uses a MOFA container label.
`modules/mofa/preprocess/main.nf`	Uses a MOFA container label.
`modules/mofa/predict/main.nf`	Uses a MOFA container label.
`modules/merge_selected_features/main.nf`	Uses a CODIA container label.
`modules/merge_result_table/main.nf`	Uses a CODIA container label.
`modules/local/samplesheet_check/main.nf`	Uses a MOGONET container label.
`modules/integrao/train/main.nf`	Uses an INTEGRAO container label.
`modules/integrao/select_feature/main.nf`	Uses an INTEGRAO container label.
`modules/integrao/preprocess/main.nf`	Uses an INTEGRAO container label.
`modules/integrao/predict/main.nf`	Uses an INTEGRAO container label.
`modules/goat/resource/usr/bin/run_goat.py`	Removes GOAT script.
`modules/goat/main.nf`	Removes GOAT process.
`modules/diablo/train/main.nf`	Uses a CODIA container label.
`modules/diablo/select_feature/main.nf`	Uses a CODIA container label.
`modules/diablo/preprocess/main.nf`	Uses a CODIA container label.
`modules/diablo/predict/main.nf`	Uses a CODIA container label.
`modules/diablo/downstream/main.nf`	Uses a CODIA container label.
`modules/cooperative_learning/train/main.nf`	Uses a CODIA container label.
`modules/cooperative_learning/select_feature/main.nf`	Uses a CODIA container label.
`modules/cooperative_learning/preprocess/main.nf`	Uses a CODIA container label.
`modules/cooperative_learning/predict/main.nf`	Uses a CODIA container label.
`modules/caret_multimodal/train/main.nf`	Uses a caret container label.
`modules/caret_multimodal/select_feature/main.nf`	Uses a caret container label.
`modules/caret_multimodal/preprocess/main.nf`	Uses a caret container label.
`modules/caret_multimodal/predict/main.nf`	Uses a caret container label.
`modules/calculate_metrics/resources/usr/bin/calculate_metrics.py`	Revises classification metrics.
`modules/calculate_metrics/main.nf`	Uses a MOGONET container label.
`conf/real_data.config`	Corrects the feature-selection parameter name.

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-    sklearn_classifier_names = ['Linear_SVM', 'Logit']
-
+    //sklearn_classifier_names = ['Linear_SVM', 'Logit', 'Decision_Tree', 'Gradient_Boost', 'Random_Forest', 'MLP', 'Hist_Gradient_Boost']
+    sklearn_classifier_names = ['Logit', 'MLP', 'Decision_Tree']


+    withLabel: rgcca    { container = 'tonyliang19/rgcca:latest'         }
+    withLabel: codia    { container = 'tonyliang19/codia:latest'         }
+    withLabel: integrao { container = 'tonyliang19/integrao:latest'      }
+    withLabel: sklearn  { container = 'tonyliang19/mogonet:latest'       } // fix: should have a new sklearn container instead, for now use mogonet one


 include { COOPERATIVE_LEARNING }  from "${subworkflowDir}/methods/cooperative_learning"
 include { DIABLO }                from "${subworkflowDir}/methods/diablo"
 include { MOFA }                  from "${subworkflowDir}/methods/mofa"
 include { RGCCA }                 from "${subworkflowDir}/methods/rgcca"


 		split_tr_te.py	${mu_path}	\
 										--split_type=${split_type} \
 										--num_splits=${num_splits}	\
+										--outcome_type=${outcome_type} \


tonyliang19 added 16 commits February 27, 2026 19:11

Merge pull request #110 from CompBio-Lab/dev

138cd5a

Major change to prepare data, seed reproduce

Merge pull request #111 from CompBio-Lab/dev

85b2b54

feat: add the final samplesheet used for the pipeline

fix: move container option to process level config, and remove stale …

e308292

…temp var option

fix: moved all container definition into config

b0c6ba5

fix: changed wrong syntax, adding args to pass in splitting modules, …

09c4905

…cli and config

fix: lint conf syntax, included back sklearn

0819287

rm: remove old files

5f7cd2e

rm: remove redundant staled configs

0ac61ac

fix: rename metric labels

2da5e23

rm: remove deprecated workflows

939ac4c

feat: sklearn to use pca50 or no reduction for more models

7944abd

fix: update method options

ec7e648

fix: include select feature for sklearn models

e5ef195

fix: correct sklearn reduction to list param rather than singleton

7c99113

fix: correct naming of parameter opt

6f0ee70

fix: make sure sklearn cv search works even with make_pipeline

0ce67f6

Copilot AI balanced review requested due to automatic review settings September 29, 2026 14:20

Copilot started reviewing on behalf of tonyliang19 September 29, 2026 14:20 View session

tonyliang19 merged commit 6b06595 into dev Sep 29, 2026
1 check passed

Copilot AI reviewed Sep 29, 2026

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Feat sklearn pca50 - #114

Feat sklearn pca50#114
tonyliang19 merged 16 commits into
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