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Fix bugs - #117
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Fix bugs#117
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Major change to prepare data, seed reproduce
feat: add the final samplesheet used for the pipeline
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🟡 Changes recommended
The centralized remote image references are incompatible with the documented offline Sockeye workflow and its preloaded named SIF files.
Review effort: Balanced
Findings: 1
What changed in this PR
Centralizes process container selection in nextflow.config, replacing project-path-based container logic with reusable labels.
Changes:
- Adds label-to-container mappings for each pipeline method.
- Updates processes to use container labels.
- Reorders Docker runtime options.
| File | Description |
|---|---|
nextflow.config |
Adds centralized container mappings and adjusts Docker options. |
modules/split_train_test/main.nf |
Uses the generic container label. |
modules/sklearn/train/main.nf |
Uses the sklearn label. |
modules/sklearn/select_feature/main.nf |
Uses the sklearn label. |
modules/sklearn/preprocess/main.nf |
Uses the sklearn label. |
modules/sklearn/predict/main.nf |
Uses the sklearn label. |
modules/rgcca/train/main.nf |
Uses the rgcca label. |
modules/rgcca/select_feature/main.nf |
Uses the rgcca label. |
modules/rgcca/preprocess/main.nf |
Uses the rgcca label. |
modules/rgcca/predict/main.nf |
Uses the rgcca label. |
modules/prepare_data/uncompress_record/main.nf |
Uses the generic label. |
modules/prepare_data/prepare_mu_data/main.nf |
Uses the generic label. |
modules/prepare_data/prepare_mae_data/main.nf |
Uses the generic label. |
modules/prepare_data/parse_metadata/main.nf |
Uses the generic label. |
modules/mogonet/train/main.nf |
Uses the mogonet label. |
modules/mogonet/select_feature/main.nf |
Uses the mogonet label. |
modules/mogonet/preprocess/main.nf |
Uses the mogonet label. |
modules/mogonet/predict/main.nf |
Uses the mogonet label. |
modules/mofa/train/main.nf |
Uses the mofa label. |
modules/mofa/select_feature/main.nf |
Uses the mofa label. |
modules/mofa/preprocess/main.nf |
Uses the mofa label. |
modules/mofa/predict/main.nf |
Uses the mofa label. |
modules/merge_selected_features/main.nf |
Uses the codia label. |
modules/merge_result_table/main.nf |
Uses the codia label. |
modules/local/samplesheet_check/main.nf |
Uses the mogonet label. |
modules/integrao/train/main.nf |
Uses the integrao label. |
modules/integrao/select_feature/main.nf |
Uses the integrao label. |
modules/integrao/preprocess/main.nf |
Uses the integrao label. |
modules/integrao/predict/main.nf |
Uses the integrao label. |
modules/diablo/train/main.nf |
Uses the codia label. |
modules/diablo/select_feature/main.nf |
Uses the codia label. |
modules/diablo/preprocess/main.nf |
Uses the codia label. |
modules/diablo/predict/main.nf |
Uses the codia label. |
modules/diablo/downstream/main.nf |
Uses the codia label. |
modules/cooperative_learning/train/main.nf |
Uses the codia label. |
modules/cooperative_learning/select_feature/main.nf |
Uses the codia label. |
modules/cooperative_learning/preprocess/main.nf |
Uses the codia label. |
modules/cooperative_learning/predict/main.nf |
Uses the codia label. |
modules/caret_multimodal/train/main.nf |
Uses the caret multimodal label. |
modules/caret_multimodal/select_feature/main.nf |
Uses the caret multimodal label. |
modules/caret_multimodal/preprocess/main.nf |
Uses the caret multimodal label. |
modules/caret_multimodal/predict/main.nf |
Uses the caret multimodal label. |
modules/calculate_metrics/main.nf |
Uses the mogonet label. |
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| withLabel: caret_multimodal { container = 'tonyliang19/caret_multimodal:latest' } | ||
| withLabel: generic { container = 'tonyliang19/save_simulate:latest' } | ||
| withLabel: mogonet { container = 'tonyliang19/mogonet:latest' } | ||
| withLabel: mofa { container = 'tonyliang19/mofa:latest' } | ||
| withLabel: rgcca { container = 'tonyliang19/rgcca:latest' } |
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