Commit d58742a2 authored by Konrad Zych's avatar Konrad Zych

Update .gitlab-ci.yml

parent bc603320
Pipeline #3033 failed with stage
in 5 minutes and 41 seconds
......@@ -21,10 +21,10 @@ test:
- Rscript 06_normalize_features.r --feat_in valFeat_sel_filtered.tsv --feat_out valFeat_sel_norm.tsv --param_out param_out.tsv --method="log.unit" --log_n0="1e-08" --sd_min_quantile="0.2" --vector_norm="2" --norm_margin="1"
- Rscript 07_add_metadata_as_predictor.r --feat_in valFeat_sel_norm.tsv --feat_out valFeat_sel_norm.tsv --metadata_in valMetaData_sel.tsv --pred_names="fobt" --std_meta="TRUE"
- Rscript 08_split_data.r --srcdir .. --label_in valLabel_sel.tsv --train_sets trainSets.tsv --test_sets testSets.tsv --num_folds="10" --resample="5" --stratify="TRUE" --inseparable="NULL" --metadata_in valMetaData_sel.tsv
- Rscript 09_train_models.r --srcdir .. --feat_in valFeat_sel_norm.tsv --label_in valLabel_sel.tsv --method="lasso" --train_sets trainSets.tsv --mlr_models_list models.RData --stratify="TRUE" --sel_criterion="auprc" --min_nonzero_coeff="2" --model models.tsv --model_matrix model.matrix.txt
- Rscript 10_make_predictions.r --srcdir .. --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --test_sets testSets.tsv --pred pred.tsv --mlr_models_list models.RData --model_matrix model.matrix.txt
- Rscript 11_evaluate_predictions.r --srcdir .. --label valLabel_sel.tsv --plot evalPlot.pdf --pred pred.tsv
- Rscript 12_interpret_model.r --srcdir .. --label valLabel_sel.tsv --feat valFeat_sel_norm.tsv --origin_feat valFeat_sel.tsv --meta valMetaData_sel.tsv --model models.RData --plot interpretation.pdf --pred pred.tsv --col_scheme="BrBG" --heatmap_type="zscore" --consens_thres="0.5"
- Rscript 09_train_models.r --srcdir .. --feat_in valFeat_sel_norm.tsv --label_in valLabel_sel.tsv --method="lasso" --train_sets trainSets.tsv --mlr_models_list models.RData --stratify="TRUE" --sel_criterion="auprc" --min_nonzero_coeff="2"
- Rscript 10_make_predictions.r --srcdir .. --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --test_sets testSets.tsv --pred pred.tsv --mlr_models_list models.RData
- Rscript 11_evaluate_predictions.r --srcdir .. --label_in valLabel_sel.tsv --plot evalPlot.pdf --pred pred.tsv
- Rscript 12_interpret_model.r --srcdir .. --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --origin_feat valFeat_sel.tsv --metadata_in valMetaData_sel.tsv --mlr_models_list models.RData --plot interpretation.pdf --pred pred.tsv --col_scheme="BrBG" --heatmap_type="zscore" --consens_thres="0.5"
only:
- master
- development
......
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