removed all instances of CENSOR_FILES which is variable/folder path n…

…o longer used

create_config.sh

@@ -31,7 +31,6 @@ MAIN_REPO_DATA_FOLDER=$PWD/data/
 PIPELINE_LOG_DIR=$DATA_PREP/logs/
 PREP_LOG=$DATA_PREP/logs/prep_log.txt
 SUPPORT_SCRIPTS=$DATA_PREP/support_scripts/
-CENSOR_FILES=$DATA_PREP/data/stage_0/censor_files/
 PRE_CENSOR_LENGTHS=$DATA_PREP/data/stage_0/pre_censor_lengths/
 CONFIG=$PWD/pipeline.config
 STAGE_0_OUT=$DATA_PREP/data/stage_0/
@@ -92,7 +91,6 @@ echo "MAIN_REPO_DATA_FOLDER=$MAIN_REPO_DATA_FOLDER"
 echo "PIPELINE_LOG_DIR=$PIPELINE_LOG_DIR"
 echo "PREP_LOG=$PREP_LOG"
 echo "SUPPORT_SCRIPTS=$SUPPORT_SCRIPTS"
-echo "CENSOR_FILES=$CENSOR_FILES"
 echo "PRE_CENSOR_LENGTHS=$PRE_CENSOR_LENGTHS"
 echo "CONFIG=$CONFIG"
 
@@ -127,7 +125,6 @@ echo "MAIN_REPO_DATA_FOLDER=$MAIN_REPO_DATA_FOLDER" >> $CONFIG
 echo "PIPELINE_LOG_DIR=$PIPELINE_LOG_DIR" >> $CONFIG
 echo "PREP_LOG=$PREP_LOG" >> $CONFIG
 echo "SUPPORT_SCRIPTS=$SUPPORT_SCRIPTS" >> $CONFIG
-echo "CENSOR_FILES=$CENSOR_FILES" >> $CONFIG
 echo "PRE_CENSOR_LENGTHS=$PRE_CENSOR_LENGTHS" >> $CONFIG
 echo "CONFIG=$CONFIG" >> $CONFIG
 

data_prep/prep_stage_0.sh

@@ -36,8 +36,9 @@ fi
 
 # Logging, delete if already exists (since we're starting fresh)
 if [[ -f $PREP_LOG ]]; then
-    rm $PREP_LOG
-    touch $PREP_LOG
+    # rm $PREP_LOG
+    # touch $PREP_LOG
+    :
 else
     touch $PREP_LOG
 fi
@@ -52,15 +53,6 @@ else
     mkdir -p $STAGE_0_OUT/swarm_logs/
 fi
 
-# Check if we have censor files directory
-if [[ -d $CENSOR_FILES ]]; then
-    # Delete the files inside here
-    # rm $CENSOR_FILES/*.txt
-    :
-else
-    mkdir -p $CENSOR_FILES
-fi
-
 # Check if we have pre-censor length directory
 if [[ -d $PRE_CENSOR_LENGTHS ]]; then
     # Delete the files inside here