Remove old PROJECT vars

workflow/qhtcp-workflow

@@ -78,7 +78,7 @@ print_help() {
 # @section Notes
 # @description
 #
-# ### TO-DO
+# ### TODO
 #
 # * Variable scoping is horrible right now
 # * I wrote this sequentially and tried to keep track the best I could
@@ -110,7 +110,7 @@ print_help() {
 # * Together they encapsulate and define the experimental design. 
 # * The QHTCPImageFolders and 'MasterPlateFiles' folder are the inputs for image analysis with EASY software. 
 # * As further described below, EASY will automatically generate a 'Results' directory (within the ExpJobs/'ExperimentJob' folder) with a name that consists of a system-generated timestamp and an optional short description provided by the user (Fig.2). The 'Results' directory is created and entered, using the "File >> New Experiment" dropdown in EASY. Multiple 'Results' files may be created (and uniquely named) within an 'ExperimentJob' folder.
-
+#
 #       **apps/easy/**
 #
 # * This directory contains the GUI-enabled MATLAB software to accomplish image analysis and growth curve fitting. 
@@ -120,7 +120,7 @@ print_help() {
 # * The /EASY directory is simply where the latest EASY version resides (additional versions in development or legacy versions may also be stored there). 
 # * The raw data inputs and result outputs for EASY are kept in the 'ExpJobs' directory. 
 # * EASY also outputs a '.mat' file that is stored in the 'matResults' folder and is named with the TimeStamp and user-provided name appended to the 'Results' folder name when 'New Experiment' is executed from the 'File' Dropdown menu in the EASY console.
-
+#
 #       **apps/ezview/**
 #
 # * This directory contains the GUI-enabled MATLAB software to conveniently and efficiently mine the raw cell array image data for a Q-HTCP experiment.
@@ -134,8 +134,6 @@ print_help() {
 # * These two file types are required in the 'MasterPlateFiles' folder, which catalogs experimental information specific to individual Jobs in the ExpJobs folder, as described further below. 
 #
 #
-# Some example decorators for markdown:
-#
 #
 # @description
 # `--project`, `--module`, `--nomodule`, and `--submodule` can be passed multiple times or with a comma-separated string
@@ -366,7 +364,6 @@ interactive_header() {
   echo "Example: SCANS_DIR=/path/to/scans OUT_DIR=/path/to/out ./qhtcp-workflow $*"
   echo ""
 
-
   # Ask to make our custom R library the default
   if [[ -z $R_LIBS_USER || $R_LIBS_USER != "$HOME/R/$SCRIPT_NAME" ]]; then
     echo "This script uses a local R library at $HOME/R/$SCRIPT_NAME"
@@ -1138,8 +1135,8 @@ easy() {
   done
 
   # Copy Templates
-  declare -gx DRUG_MEDIA_FILE="$EASY_RESULTS_DIR/DrugMedia_$PROJECT.xls"
-  declare -gx MASTER_PLATE_FILE="$EASY_RESULTS_DIR/MasterPlate_$PROJECT.xls"
+  declare -gx DRUG_MEDIA_FILE="$EASY_RESULTS_DIR/DrugMedia_$PROJECT_NAME.xls"
+  declare -gx MASTER_PLATE_FILE="$EASY_RESULTS_DIR/MasterPlate_$PROJECT_NAME.xls"
   rsync -a "$EASY_DIR"/{figs,PTmats} "$EASY_RESULTS_DIR"
 
   # Ask the user to launch EASYconsole.m in MATLAB
@@ -1345,7 +1342,7 @@ qhtcp() {
     for s in "${STUDIES_NUMS[@]}"; do
       # Trying to match old ExpFrontend formatting
       printf "%s\t" \
-        "${DATE//_/}" "$PROJECT" "$QHTCP_PROJECT_DIR" "Exp$s" \
+        "${DATE//_/}" "$PROJECT_NAME" "$QHTCP_PROJECT_DIR" "Exp$s" \
         "$PROJECT_DATE" "$PROJECT_SCANS_DIR" "$EASY_RESULTS_DIR" "${f##*/}" \
         >> "$STUDIES_ARCHIVE_FILE"
     done
@@ -1955,16 +1952,14 @@ submodule get_studies
 # * Expanded into a file that stores all project/study settings (database)
 # * I had to had a new line to the end of StudyInfo.csv, may break things?
 #
-# Example:
-#   ExpNumb,ExpLabel,BackgroundSD,ZscoreJoinSD,AnalysisBy
-#   1,ExpName1,NA,NA,UserInitials
-#   2,ExpName2,NA,NA,UserInitials
-#   3,ExpName3,NA,NA,UserInitials
+#    
+#
 # @exitcode 0 If one or more studies found
 # @exitcode 1 If no studies found
 # @set STUDIES_NUMS array Contains Exp numbers
 # @set NUM_STUDIES int Number of existing studies
 # @arg $1 string File to read
+#
 get_studies() {
   debug "Running: ${FUNCNAME[0]}"
   declare -ga STUDIES_NUMS=()