test(picard): Add failing test for markduplicates

tests/software/picard/main.nf

@@ -37,3 +37,12 @@ workflow test_picard_markduplicates  {
 
     PICARD_MARKDUPLICATES ( input )
 }
+
+workflow test_picard_markduplicates_not_sorted  {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
+
+    PICARD_MARKDUPLICATES ( input )
+}

tests/software/picard/test.yml

@@ -33,3 +33,11 @@
     - path: output/picard/test.MarkDuplicates.metrics.txt
     - path: output/picard/test.bam
       md5sum: 50407a1ee722f2bf6a20471c8a7fd6b0
+
+- name: Run picard MarkDuplicates without a sorted bam file so it fails
+  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard_markduplicates
+    - should fail
+  exit_code: 1