luslab-umitools | Rudimentary hash checking of files

tools/umi_tools/test/main.nf

@@ -49,4 +49,17 @@ workflow {
 
     // Collect file names and view output
     umitools_dedup.out.dedupBam | view
+}
+
+workflow.onComplete {
+    def proc = "$baseDir/verify-checksum.sh $baseDir/../../../results/umitools/dedup/*.bai $baseDir/output/*.bai".execute()
+    def b = new StringBuffer()
+    proc.consumeProcessErrorStream(b)
+
+    log.info proc.text
+
+    errorString = b.toString()
+    if(errorString != '')
+        log.error errorString
+        exit 1
 }

tools/umi_tools/test/verify-checksum.sh

@@ -0,0 +1,40 @@
+#!/bin/sh
+
+if [ -z "$1" ]
+  then
+    echo "No check pattern argument supplied" >&2
+    exit 1
+fi
+
+if [ -z "$2" ]
+  then
+    echo "No verify pattern argument supplied" >&2
+    exit 1
+fi
+
+checkfiles=$1
+infiles=$2
+#echo $checkfiles
+#echo $infiles
+
+echo '\nCalculating check file hashes...'
+md5sum $checkfiles
+
+echo '\nCalculating input file hashes...'
+md5sum $infiles
+
+echo '\nComparing hash of file of hashes...'
+checkver=$(md5sum $checkfiles | awk '{print $1}' | md5sum | awk '{print $1}')
+echo $checkver
+
+inver=$(md5sum $infiles | awk '{print $1}' | md5sum | awk '{print $1}')
+echo $inver
+
+if [ "$checkver" == "$inver" ]
+then
+  echo "Hashes match"
+  exit 0
+else
+  echo "Hashes do not match" >&2
+  exit 1
+fi