From 6e99e69f8c648850e1074aad2e2bb1374a9cefbf Mon Sep 17 00:00:00 2001
From: Meng Li <34143965+Meng6@users.noreply.github.com>
Date: Fri, 15 May 2020 17:59:14 -0400
Subject: [PATCH] Save cleaned features with different data cleaning
 threasholds under different folders

---
 rules/models.snakefile | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/rules/models.snakefile b/rules/models.snakefile
index ec3e17af..500903ea 100644
--- a/rules/models.snakefile
+++ b/rules/models.snakefile
@@ -61,13 +61,13 @@ rule clean_features_for_individual_model:
     input:
         rules.merge_features_for_individual_model.output
     params:
-        cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
-        cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
-        rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
-        days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
-        days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"]
+        cols_nan_threshold = "{cols_nan_threshold}",
+        cols_var_threshold = "{cols_var_threshold}",
+        days_before_threshold = "{days_before_threshold}",
+        days_after_threshold = "{days_after_threshold}",
+        rows_nan_threshold = "{rows_nan_threshold}",
     output:
-        "data/processed/{pid}/data_for_individual_model/{source}_{day_segment}_clean.csv"
+        "data/processed/{pid}/data_for_individual_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_clean.csv"
     script:
         "../src/models/clean_features_for_model.R"
 
@@ -75,13 +75,13 @@ rule clean_features_for_population_model:
     input:
         rules.merge_features_for_population_model.output
     params:
-        cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
-        cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
-        rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
-        days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
-        days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"]
+        cols_nan_threshold = "{cols_nan_threshold}",
+        cols_var_threshold = "{cols_var_threshold}",
+        days_before_threshold = "{days_before_threshold}",
+        days_after_threshold = "{days_after_threshold}",
+        rows_nan_threshold = "{rows_nan_threshold}",
     output:
-        "data/processed/data_for_population_model/{source}_{day_segment}_clean.csv"
+        "data/processed/data_for_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_clean.csv"
     script:
         "../src/models/clean_features_for_model.R"