Feat sklearn pca50

[tonyliang19]

• removing staled codes
• updating sklearn for simple baselines and allow for reduced dataset via pca

[Copilot]

Pull request overview

This PR modernizes the pipeline by removing legacy simulation/method scaffolding, wiring an outcome_type into splitting to support survival-style outcomes, and extending the sklearn baseline to optionally run a PCA-based dimensionality reduction (e.g., pca50). It also refactors many processes to rely on label-based container selection from nextflow.config instead of inline container directives.

Changes:

• Add params.outcome_type and propagate it through the splitting workflow into the split script CLI.
• Extend sklearn training to accept a --reduction option and encode reduction into model/log artifacts.
• Remove stale simulation workflows/method stubs and standardize module container selection via labels in nextflow.config.

Reviewed changes

Copilot reviewed 54 out of 66 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
subworkflows/splitting/main.nf	Passes outcome_type into split module
subworkflows/simulation/main.nf	Removed legacy simulation subworkflow
subworkflows/prepare_data/main.nf	Removes simulation include
subworkflows/methods/sklearn/main.nf	Adds reduction channel, passes into training
subworkflows/methods/sgmr/main.nf	Removed SGMR stub workflow
subworkflows/cross_validation/r/main.nf	Removes SGMR from R CV include list
subworkflows/cross_validation/python/main.nf	Removes GOAT execution path; formatting tweaks
subworkflows/cross_validation/main.nf	Updates shouldRunPython() gating logic
nextflow.config	Adds new params, updates sklearn params, centralizes containers by label
modules/split_train_test/resources/usr/bin/split_tr_te.py	Adds outcome_type + event_col CLI handling
modules/split_train_test/main.nf	Adds outcome_type input and passes CLI flag; switches to label-based container
modules/sklearn/train/resources/usr/bin/sklearn_train.py	Adds PCA/ColumnTransformer-based reduction pipeline
modules/sklearn/train/resources/usr/bin/load_classifier_class.py	Refactors classifier registry; adds MLP + HistGradientBoost
modules/sklearn/train/resources/usr/bin/combine_mdata2df.py	Returns modality names for downstream reduction
modules/sklearn/train/main.nf	Adds reduction to tagging/output identity; passes --reduction
modules/sklearn/select_feature/main.nf	Switches to label-based container selection
modules/sklearn/preprocess/main.nf	Switches to label-based container selection
modules/sklearn/predict/main.nf	Switches to label-based container selection
modules/simulation/simulate_mvn_data/resources/usr/bin/unique_matrices.R	Removed legacy simulation script
modules/simulation/simulate_mvn_data/resources/usr/bin/simulate_data.R	Removed legacy simulation script
modules/simulation/simulate_mvn_data/resources/usr/bin/gen_simul_metadata.R	Removed legacy simulation script
modules/simulation/simulate_mvn_data/resources/usr/bin/debug_simulate_data.R	Removed legacy simulation script
modules/simulation/simulate_mvn_data/main.nf	Removed MVN simulation module
modules/simulation/simulate_intersim/resources/usr/bin/simulate_InterSIM.R	Removed InterSIM simulation script
modules/simulation/simulate_intersim/resources/usr/bin/save_mudata.py	Removed InterSIM helper script
modules/simulation/simulate_intersim/main.nf	Removed InterSIM simulation module
modules/rgcca/train/main.nf	Switches to label-based container selection
modules/rgcca/select_feature/main.nf	Switches to label-based container selection
modules/rgcca/preprocess/main.nf	Switches to label-based container selection
modules/rgcca/predict/main.nf	Switches to label-based container selection; removes stray label
modules/prepare_data/uncompress_record/main.nf	Switches to label-based container selection
modules/prepare_data/prepare_mu_data/main.nf	Switches to label-based container selection
modules/prepare_data/prepare_mae_data/main.nf	Switches to label-based container selection
modules/prepare_data/parse_metadata/main.nf	Switches to label-based container selection
modules/mogonet/train/main.nf	Switches to label-based container selection
modules/mogonet/select_feature/main.nf	Switches to label-based container selection
modules/mogonet/preprocess/main.nf	Switches to label-based container selection
modules/mogonet/predict/main.nf	Switches to label-based container selection
modules/mofa/train/main.nf	Switches to label-based container selection
modules/mofa/select_feature/main.nf	Switches to label-based container selection
modules/mofa/preprocess/main.nf	Switches to label-based container selection
modules/mofa/predict/main.nf	Switches to label-based container selection
modules/merge_selected_features/main.nf	Switches to label-based container selection
modules/merge_result_table/main.nf	Switches to label-based container selection
modules/local/samplesheet_check/main.nf	Switches to label-based container selection
modules/integrao/train/main.nf	Switches to label-based container selection
modules/integrao/select_feature/main.nf	Switches to label-based container selection
modules/integrao/preprocess/main.nf	Switches to label-based container selection
modules/integrao/predict/main.nf	Switches to label-based container selection
modules/goat/main.nf	Removed GOAT module process
modules/diablo/train/main.nf	Switches to label-based container selection
modules/diablo/select_feature/main.nf	Switches to label-based container selection
modules/diablo/preprocess/main.nf	Switches to label-based container selection
modules/diablo/predict/main.nf	Switches to label-based container selection
modules/diablo/downstream/main.nf	Switches to label-based container selection
modules/cooperative_learning/train/main.nf	Switches to label-based container selection
modules/cooperative_learning/select_feature/main.nf	Switches to label-based container selection
modules/cooperative_learning/preprocess/main.nf	Switches to label-based container selection
modules/cooperative_learning/predict/main.nf	Switches to label-based container selection
modules/caret_multimodal/train/main.nf	Switches to label-based container selection
modules/caret_multimodal/select_feature/main.nf	Switches to label-based container selection
modules/caret_multimodal/preprocess/main.nf	Switches to label-based container selection
modules/caret_multimodal/predict/main.nf	Switches to label-based container selection
modules/calculate_metrics/resources/usr/bin/calculate_metrics.py	Expands/renames computed metric set
modules/calculate_metrics/main.nf	Switches to label-based container selection

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