Finish R script linting

workflow/qhtcp-workflow

@@ -1620,7 +1620,12 @@ gta() {
   for combo in "${study_combos[@]}"; do
     # Split on comma and assign to array
     IFS=',' read -ra studies <<< "$combo"
-    r_gta_pairwiselk "${studies[0]}" "${studies[1]}" "$STUDY_INFO_FILE" "$gta_out_dir"
+    r_gta_pairwiselk \
+      "${studies[0]}" \
+      "${studies[1]}" \
+      "$STUDY_INFO_FILE" \
+      "Average_GOTerms_All.csv" \
+      "$gta_out_dir"
   done
 
   # All studies
@@ -1660,17 +1665,18 @@ wrapper r_gta
 #
 # TODO
 #
-#   * Is GTAtemplate.R actually a template?
-#   * Do we need to allow user customization?
+# * Is GTAtemplate.R actually a template?
+# * Do we need to allow user customization?
 #
-# Files
+# INPUT
 #
-#   * [gene_association.sgd](https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd)
-#   * go_terms.tab
+# * [gene_association.sgd](https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd)
+# * go_terms.tab
 #
-# Output
+# OUTPUT
+#
+# * Average_GOTerms_All.csv
 #
-#   *
 #
 # @arg $1 string Exp# name
 # @arg $2 string ZScores_Interaction.csv file
@@ -1683,7 +1689,7 @@ r_gta() {
   cat <<-EOF
 
 	EOF
-  script="$APPS_DIR/r/GTAtemplate.R"
+  script="$APPS_DIR/r/gtaTemplate.R"
   [[ -d $5 ]] || mkdir -p "$5"
   debug "$RSCRIPT $script $*"
   "$RSCRIPT" "$script" \
@@ -1701,16 +1707,18 @@ wrapper r_gta_pairwiselk
 #
 # TODO
 #
-#   * Should move directory creation from PairwiseLK.R to gta module
+# * Move directory creation from PairwiseLK.R to gta module
+# * Needs better output filenames and directory organization
+# * Needs more for looping to reduce verbosity
 #
-# Files
+# INPUT
 #
-#   * 
-#   * 
+# * Average_GOTerms_All.csv
+# * 
 #
 # Output
 #
-#   *
+# *
 #
 # This wrapper:
 #
@@ -1724,7 +1732,7 @@ wrapper r_gta_pairwiselk
 # @arg $4 string output directory
 #
 r_gta_pairwiselk() {
-  debug "Running: ${FUNCNAME[0]}"
+  debug "Running: ${FUNCNAME[0]} $*"
   cat <<-EOF
 
 	EOF
@@ -1734,7 +1742,12 @@ r_gta_pairwiselk() {
   [[ -d $4 ]] || mkdir -p "$4"
 
   debug "$RSCRIPT $script $*"
-  "$RSCRIPT" "$script" "$@"
+  "$RSCRIPT" "$script" \
+    "$1" \
+    "$2" \
+    "$3" \
+    "$4" \
+    "${@:5}"
 }
 
 
@@ -1842,6 +1855,10 @@ r_interactions() {
 wrapper r_join_interactions
 # @description JoinInteractExps3dev.R creates REMcRdy_lm_only.csv and Shift_only.csv
 #
+# TODO
+# * Needs more loops to reduce verbosity
+#
+#
 # Output
 #
 # * REMcRdy_lm_only.csv