First attempt at script-run-workflow

workflow/templates/qhtcp/Code/RenameFiles2.sh

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+#ReNameFiles2.sh renames files in the /ZScores and /QC folders of each EXP_ to reflect the user labeling of the Exp_'s
+#The ZScores_Interaction.csv file is required by many processes and therefore its name must be preserved
+pwd
+#Preserve ZScores_Interaction.csv in ZScores_Interaction.csvx temporary file
+cp ZScores_Interaction.csv ZScores_Interaction.csvx
+#Determine which /Exp_ this script is called from
+cd ../
+ExpDir="${PWD##*/}"
+cd ZScores
+
+if [ "$ExpDir" = "Exp1" ];then j=1;fi #Cannot have spaces in declaratives. Must have spaces in compare statements
+if [ "$ExpDir" = "Exp2" ];then j=2;fi #Must use j to make value an integer
+if [ "$ExpDir" = "Exp3" ];then j=3;fi
+if [ "$ExpDir" = "Exp4" ];then j=4;fi
+echo $j  #j makes value an integer for use in the following extraction of data from StudyInfo.csv spreadsheet
+#-------------
+#Extract the user's experiment Name stored in StudyInfo.csv found in../Code folder
+eCollection=( $(cut -d ',' -f2 ../../Code/StudyInfo.csv) )
+expName="${eCollection[$j]}"
+echo $expName
+
+#Remove double quotes that are an artifact of the .csv spreadsheet cells
+temp=`echo $expName | sed 's/.\(.*\)/\1/' | sed 's/\(.*\)./\1/'`
+expName=$temp
+echo $expName  #display the extracted user experiment label without the double quotes
+
+#Rename csv files
+#The Sumary...csv files have a leading "white space" that the basename removes. Therefore must directly rename the #Summary files without the whitespace.
+mv  " "SummaryStats_BackgroundStrains.csv SummaryStats_BackgroundStrains.csv
+mv  " "SummaryStats_ALLSTRAINS.csv SummaryStats_ALLSTRAINS.csv
+for i in $(ls *.csv); do
+mv $i $(basename $i .csv)___$expName.csv
+done
+
+#restore ZScores_Interaction.csv
+mv ZScores_Interaction.csvx ZScores_Interaction.csv
+
+#Rename pdf files
+for i in $(ls *.pdf); do
+mv $i $(basename $i .pdf)___$expName.pdf    
+done
+
+#Rename .html files
+for i in $(ls *.html); do
+mv $i $(basename $i .html)___$expName.html   
+done
+
+pwd
+echo $expName
+
+#Rename csv files
+cd QC #Step into the ../QC directory
+#Rename csv files#Rename csv files
+for i in $(ls *.csv); do
+mv $i $(basename $i .csv)___$expName.csv
+done
+#Rename pdf files
+for i in $(ls *.pdf); do
+mv $i $(basename $i .pdf)___$expName.pdf    
+done
+#Rename .html files
+for i in $(ls *.html); do
+mv $i $(basename $i .html)___$expName.html   
+done
+
+cd .. #Return to ../ZScores folder
+
+
+