deleted notes

Author: JudithBernett

modules/local/params_check/main.nf

@@ -18,6 +18,8 @@ process PARAMS_CHECK {
     val path_data
 
     output:
+    // note: this needs to be a value even though it is a path because otherwise, nextflow will interpret it only
+    // relatively to the work directory and as this path is outside the work directory, it will fail.
     val path_data,     emit: path_data
 
     when:

modules/local/predict_full/main.nf

@@ -7,6 +7,8 @@ process PREDICT_FULL {
     input:
     tuple path(cross_study_datasets), val(model_name), val(test_mode), val(split_id), path(split_dataset), path(hpam_combi)
     val(response_transformation)
+    // note: this needs to be a value even though it is a path because otherwise, nextflow will interpret it only
+    // relatively to the work directory and as this path is outside the work directory, it will fail.
     val(path_data)
 
     output:

modules/local/randomization_test/main.nf

@@ -6,6 +6,8 @@ process RANDOMIZATION_TEST {
 
     input:
     tuple val(model_name), val(test_mode), val(split_id), path(split_dataset), path(best_hpams), path(randomization_views)
+    // note: this needs to be a value even though it is a path because otherwise, nextflow will interpret it only
+    // relatively to the work directory and as this path is outside the work directory, it will fail.
     val(path_data)
     val(randomization_type)
     val(response_transformation)

modules/local/robustness_test/main.nf

@@ -6,6 +6,8 @@ process ROBUSTNESS_TEST {
 
     input:
     tuple val(model_name), val(test_mode), val(split_id), path(split_dataset), path(best_hpams), val(robustness_iteration)
+    // note: this needs to be a value even though it is a path because otherwise, nextflow will interpret it only
+    // relatively to the work directory and as this path is outside the work directory, it will fail.
     val(path_data)
     val(randomization_type)
     val(response_transformation)

modules/local/train_and_predict_cv/main.nf

@@ -5,6 +5,8 @@ process TRAIN_AND_PREDICT_CV {
 
     input:
     tuple val(model_name), val(test_mode), path(cv_data), path(hyperparameters)
+    // note: this needs to be a value even though it is a path because otherwise, nextflow will interpret it only
+    // relatively to the work directory and as this path is outside the work directory, it will fail.
     val path_data
     val response_transformation