From 4eca77d63b6498d0e65700976766c4732844fddc Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 16 May 2022 17:39:33 -0500
Subject: [PATCH] Add CAT_FASTQ tests for a single pair of files

The test is written to expect that the input files will be renamed, but the
contents will remain the same, i.e. the test uses the md5 hash of the input
files.
---
 tests/modules/cat/fastq/main.nf  | 12 ++++++++++++
 tests/modules/cat/fastq/test.yml | 11 +++++++++++
 2 files changed, 23 insertions(+)

diff --git a/tests/modules/cat/fastq/main.nf b/tests/modules/cat/fastq/main.nf
index b8c739e4..ec5a4d0d 100644
--- a/tests/modules/cat/fastq/main.nf
+++ b/tests/modules/cat/fastq/main.nf
@@ -56,3 +56,15 @@ workflow test_cat_fastq_single_end_single_file {
 
     CAT_FASTQ( input )
 }
+
+workflow test_cat_fastq_paired_end_single_file {
+    input = [
+        [ id:'test', single_end: false ],
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    CAT_FASTQ( input )
+}
diff --git a/tests/modules/cat/fastq/test.yml b/tests/modules/cat/fastq/test.yml
index d9fe33e2..4952788f 100644
--- a/tests/modules/cat/fastq/test.yml
+++ b/tests/modules/cat/fastq/test.yml
@@ -46,3 +46,14 @@
   files:
     - path: ./output/cat/test.merged.fastq.gz
       md5sum: e325ef7deb4023447a1f074e285761af
+
+- name: cat fastq paired-end-single-file
+  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end_single_file -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test_1.merged.fastq.gz
+      md5sum: e325ef7deb4023447a1f074e285761af
+    - path: ./output/cat/test_2.merged.fastq.gz
+      md5sum: 22342ee8873e5bfa51b4707bb1d56ec6