Output changed to mach GA4GH checker

pcawg-bwa-mem-aligner/checker/pcawg-bwa-mem-aligner.checker.cwl

@@ -4,7 +4,7 @@ class: CommandLineTool
 
 hints:
 - class: DockerRequirement
-  dockerPull: quay.io/baminou/pcawg-bwa-mem-aligner-ga4gh-result-checker:1.0
+  dockerPull: quay.io/baminou/pcawg-bwa-mem-aligner-ga4gh-result-checker:2.0
 
 inputs:
   result_files:
@@ -15,15 +15,15 @@ inputs:
       position: 1
 
 outputs:
-  report_file:
+  stdout_log:
     type: File
     outputBinding:
-      glob: results.json
-    doc: A text file contains report of the checker
-  report_log:
+      glob: log.stdout
+    doc: File containing result
+  stderr_log:
     type: File
     outputBinding:
-      glob: log.txt
-    doc: A log file contains additional details of checker report
+      glob: log.stderr
+    doc: File containing error result
 
-baseCommand: ["bash", "/usr/local/bin/pcawg-bwa-mem-result-checker.sh"]
+baseCommand: ["bash", "/usr/local/bin/pcawg-bwa-mem-result-checker.sh"]

pcawg-bwa-mem-aligner/checker/pcawg-bwa-mem-result-checker.sh

@@ -35,12 +35,13 @@ if [ $(check_md5 <(cat $unmapped_bai1) <(cat $unmapped_bai2)) -eq 0 ];then echo
 if [ $(check_md5 <(cat $normal_metrics1) <(cat $normal_metrics2)) -eq 0 ];then echo "overall: false" > log.txt;echo "mismatch result found in "$normal_metrics2 >> log.txt;flag=1;fi
 if [ $(check_md5 <(cat $unmapped_metrics1) <(cat $unmapped_metrics2)) -eq 0 ];then echo "overall: false" > log.txt;echo "mismatch result found in "$unmapped_metrics2 >> log.txt;flag=1;fi
 
+touch log.stdout
+touch log.stderr
 if [ $flag -eq 0 ]
 then
-	echo "overall: true" > log.txt
-	echo "{\"overall\": true}" > results.json
+        echo "{\"overall\": true}" > log.stdout
+        exit 0
 else
-	echo "{\"overall\": false}" > results.json
-fi
-
-touch test.json
+        echo "{\"overall\": false}" >> log.stderr
+        exit 1
+fi