Commit 103393fa authored by Konrad Zych's avatar Konrad Zych
Browse files

Update .gitlab-ci.yml

parent 7ed7b9d1
Pipeline #4143 passed with stage
in 24 seconds
......@@ -10,7 +10,7 @@ build:
stage: build
script:
- R CMD build ./ --no-build-vignettes
- R CMD INSTALL SIAMCAT_0.99.0.tar.gz
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
- mv SIAMCAT_* ./Rscript_flavor
- cd Rscript_flavor
- wget http://congo.embl.de/downloads/siamcat_test_data.tar.gz
......@@ -24,7 +24,7 @@ preprocess_data:
stage: preprocess_data
before_script:
- cd Rscript_flavor
- R CMD INSTALL SIAMCAT_0.99.0.tar.gz
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
script:
- Rscript 01_validate_data.r --metadata_in num_metadata_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --metadata_out valMetaData.tsv --label_in label_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --label_out valLabel.tsv --feat_in feat_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --feat_out valFeat.tsv
- Rscript 02_select_samples.r --metadata_in valMetaData.tsv --metadata_out valMetaData_sel.tsv --label_in valLabel.tsv --label_out valLabel_sel.tsv --feat_in valFeat.tsv --feat_out valFeat_sel.tsv --filter_var="age" --allowed_range="[0,120]"
......@@ -47,7 +47,7 @@ train_model:
stage: train_model
before_script:
- cd Rscript_flavor
- R CMD INSTALL SIAMCAT_0.99.0.tar.gz
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
script:
- Rscript 09_train_models.r --feat_in valFeat_sel_norm.tsv --label_in valLabel_sel.tsv --method="lasso" --data_split dataSplit.Rdata --mlr_models_list models.RData --stratify="TRUE" --sel_criterion="auprc" --min_nonzero_coeff="2"
......@@ -64,7 +64,7 @@ make_predictions:
stage: make_predictions
before_script:
- cd Rscript_flavor
- R CMD INSTALL SIAMCAT_0.99.0.tar.gz
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
script:
- Rscript 10_make_predictions.r --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --data_split dataSplit.Rdata --pred pred.tsv --mlr_models_list models.RData
......@@ -81,7 +81,7 @@ evaluate_interpret:
stage: evaluate_interpret
before_script:
- cd Rscript_flavor
- R CMD INSTALL SIAMCAT_0.99.0.tar.gz
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
script:
- Rscript 11_evaluate_predictions.r --label_in valLabel_sel.tsv --plot evalPlot.pdf --pred pred.tsv
- Rscript 12_interpret_model.r --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"
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment