Add xml_validator test for IsoSeq

src/wdlci/wdl_tests/count_columns.wdl

@@ -26,8 +26,9 @@ task count_columns {
 			current_run_output_column_count=$(sed 's;,;\t;g' ~{current_run_output} | awk '{print NF}' | sort -nu | tail -n 1)
 			validated_output_column_count=$(sed 's;,;\t;g' ~{validated_output} | awk '{print NF}' | sort -nu | tail -n 1)
 		else
-			current_run_output_column_count=$(awk '{print NF}' ~{current_run_output} | sort -nu | tail -n 1)
-			validated_output_column_count=$(awk '{print NF}' ~{validated_output} | sort -nu | tail -n 1)
+			# Disregard headers starting with `#`
+			current_run_output_column_count=$(sed '/^#/d' ~{current_run_output} | awk '{print NF}' | sort -nu | tail -n 1)
+			validated_output_column_count=$(sed '/^#/d' ~{validated_output} | awk '{print NF}' | sort -nu | tail -n 1)
 		fi
 
 		if [[ "$current_run_output_column_count" != "$validated_output_column_count" ]]; then

src/wdlci/wdl_tests/xml_validator.wdl

@@ -0,0 +1,47 @@
+version 1.0
+
+# Parse and validate XML file
+# Input type: XML files
+
+task xml_validator {
+	input {
+		File current_run_output
+		File validated_output
+	}
+
+	Int disk_size = ceil(size(current_run_output, "GB") + size(validated_output, "GB") + 50)
+
+	command <<<
+		set -euo pipefail
+
+		err() {
+			message=$1
+
+			echo -e "[ERROR] $message" >&2
+		}
+
+		if ! xmllint --noout ~{validated_output}; then
+			err "Validated XML file: [~{basename(validated_output)}] is invalid"
+			exit 1
+		else
+			if ! xmllint --noout ~{current_run_output}; then
+				err "Current run XML file: [~{basename(current_run_output)}] is invalid"
+				exit 1
+			else
+				echo "Current run XML file: [~{basename(current_run_output)}] is valid"
+			fi
+		fi
+	>>>
+
+	output {
+	}
+
+	runtime {
+		docker: "dnastack/dnastack-wdl-ci-tools:0.0.1"
+		cpu: 1
+		memory: "3.75 GB"
+		disk: disk_size + " GB"
+		disks: "local-disk " + disk_size + " HDD"
+		preemptible: 1
+	}
+}