From d1a77b2fb2020f46e04d0c4a67fda633237e73a2 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Tue, 24 Nov 2020 19:38:49 -0600
Subject: [PATCH] test(picard): Add failing test for markduplicates

---
 tests/software/picard/main.nf  | 9 +++++++++
 tests/software/picard/test.yml | 8 ++++++++
 2 files changed, 17 insertions(+)

diff --git a/tests/software/picard/main.nf b/tests/software/picard/main.nf
index 54cf3965..d291de6d 100644
--- a/tests/software/picard/main.nf
+++ b/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 )
+}
diff --git a/tests/software/picard/test.yml b/tests/software/picard/test.yml
index 97eef8ea..4a813f37 100644
--- a/tests/software/picard/test.yml
+++ b/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