Update runner

runner.sh

 #!/bin/bash
 # Example script for the INF pipeline
 
-THREADS=12
+CORES=12
 
 OUTFOLDER=results
 DATAFOLDER=data
-DATASET=tcga_breast
+DATASET=tcga_aml
 LAYER1=gene
-LAYER2=cnv
-TARGET=ER
-MODEL=LSVM
+LAYER2=meth
+LAYER3=mirna
+TARGET=OS
+MODEL=randomForest
 N_SPLITS_START=0
 N_SPLITS_END=10
 
-RANDOM_LABELS=true
+RANDOM_LABELS=false
 
 # go!
 
 for (( i=$N_SPLITS_START; i<$N_SPLITS_END; i++ ))
 do
-    snakemake -s Snakefile_split --cores $THREADS --config datafolder=$DATAFOLDER outfolder=$OUTFOLDER dataset=$DATASET target=$TARGET layer1=$LAYER1 layer2=$LAYER2  model=$MODEL random=$RANDOM_LABELS split_id=$i  -p 
+    snakemake -s Snakefile_split --cores $CORES --config datafolder=$DATAFOLDER outfolder=$OUTFOLDER dataset=$DATASET target=$TARGET layer1=$LAYER1 layer2=$LAYER2 layer3=$LAYER3 model=$MODEL random=$RANDOM_LABELS split_id=$i  -p 
 done
 
 if [ $RANDOM_LABELS = true ]
@@ -29,16 +30,16 @@ fi
 
 for MODE in juxt rSNF rSNFi single
 do
-    python postprocessing/compute_all_metrics.py --outfolder $OUTFOLDER --dataset $DATASET --target $TARGET --layers $LAYER1 $LAYER2 --model $MODEL --n_splits_end $N_SPLITS_END --n_splits_start $N_SPLITS_START --mode $MODE
+    python postprocessing/compute_all_metrics.py --outfolder $OUTFOLDER --dataset $DATASET --target $TARGET --layers $LAYER1 $LAYER2 $LAYER3 --model $MODEL --n_splits_end $N_SPLITS_END --n_splits_start $N_SPLITS_START --mode $MODE
 done
 
 
 for MODE in juxt rSNF 
 do
-    python postprocessing/borda_global_juxt_rSNF.py --datafolder $DATAFOLDER --outfolder $OUTFOLDER --dataset $DATASET --target $TARGET --layers $LAYER1 $LAYER2 --model $MODEL --n_splits_end $N_SPLITS_END --n_splits_start $N_SPLITS_START --mode $MODE
+    python postprocessing/borda_global_juxt_rSNF.py --datafolder $DATAFOLDER --outfolder $OUTFOLDER --dataset $DATASET --target $TARGET --layers $LAYER1 $LAYER2 $LAYER3 --model $MODEL --n_splits_end $N_SPLITS_END --n_splits_start $N_SPLITS_START --mode $MODE
 done
 
-python postprocessing/borda_global_rSNFi.py --datafolder $DATAFOLDER --outfolder $OUTFOLDER --dataset $DATASET --target $TARGET --layers $LAYER1 $LAYER2 --model $MODEL --n_splits_end $N_SPLITS_END --n_splits_start $N_SPLITS_START --mode rSNFi
+python postprocessing/borda_global_rSNFi.py --datafolder $DATAFOLDER --outfolder $OUTFOLDER --dataset $DATASET --target $TARGET --layers $LAYER1 $LAYER2 $LAYER3 --model $MODEL --n_splits_end $N_SPLITS_END --n_splits_start $N_SPLITS_START --mode rSNFi