Update for bats testing.

workflow/main.nf

@@ -496,7 +496,7 @@ process plotProfile {
   script:
   """
   module load deeptools/2.5.0.1
-  bash $baseDir/scripts/plot_profile.sh $gtfFile
+  bash $baseDir/scripts/plot_profile.sh
   """
 }
 

workflow/scripts/plot_profile.sh

 #!/bin/bash
 #plot_profile.sh
 
-bws=$(ls *.bw)
-gtf=$(ls *.gtf *.bed)
-
-computeMatrix reference-point \
-	--referencePoint TSS \
-	-S $bws \
-	-R $gtf \
-	--skipZeros \
-	-o computeMatrix.gz
-	-p max/2
-
-plotProfile -m computeMatrix.gz \
-	-out plotProfile.png \
+raise()
+{
+  echo "${1}" >&2
+}
+
+check_tools() {
+	raise "
+   Checking for required libraries and components on this system
+   "
+	 deeptools --version &> version_deeptools.txt
+	 if [ $? -gt 0 ]
+	 	then
+			raise "Missing deeptools"
+			return 1
+		fi
+}
+
+compute_matrix() {
+  raise "
+  Computing matrix on ${1} using ${2}
+  "
+
+	computeMatrix reference-point \
+		--referencePoint TSS \
+		-S ${1} \
+		-R ${2} \
+		--skipZeros \
+		-o computeMatrix.gz \
+		-p max/2
+
+  if [ $? -gt 0 ]
+  then
+    raise "Problem building matrix"
+    return 1
+  fi
+}
+
+plot_profile() {
+  raise "
+  Plotting profile
+  "
+
+	plotProfile -m computeMatrix.gz \
+		-out plotProfile.png
+
+  if [ $? -gt 0 ]
+  then
+    raise "Problem plotting"
+    return 1
+  fi
+}
+
+
+run_main() {
+	bws=$(ls *.bw)
+	gtf=$(ls *.gtf *.bed)
+
+  check_tools || exit 1
+
+	compute_matrix "${bws}" "${gtf}" || return 1
+
+	plot_profile || return 1
+
+  raise "ALL COMPLETE"
+}
+
+if [[ "${BASH_SOURCE[0]}" == "${0}" ]]
+then
+  run_main
+  if [ $? -gt 0 ]
+  then
+    exit 1
+  fi
+fi

workflow/tests/plot_profile.bats

+#!/opt/bats/libexec/bats-core/ bats
+
+profile_script="./worflow/scripts/plot_profile.sh"
+
+setup() {
+  module load deeptools/2.5.0.1
+}
+
+@test "Test deeptools present" {
+  source ${profile_script}
+  run check_tools
+  assert_success
+}
+
+@test "Test matrix generation" {
+  source ${profile_script}
+  run check_tools
+  assert_success
+}