From 5a2e3035220f30ab2d6fec5ded5a365e327248e4 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 13 May 2022 19:16:50 +0200
Subject: [PATCH] add PE sorted test

---
 tests/modules/bowtie2/align/main.nf | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/tests/modules/bowtie2/align/main.nf b/tests/modules/bowtie2/align/main.nf
index 75ab33ac..4f08b533 100644
--- a/tests/modules/bowtie2/align/main.nf
+++ b/tests/modules/bowtie2/align/main.nf
@@ -51,6 +51,22 @@ workflow test_bowtie2_align_paired_end {
     BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
 }
 
+workflow test_bowtie2_align_paired_end_sorted {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_unaligned = false
+    sort = true
+
+    BOWTIE2_BUILD ( fasta )
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
+}
+
 workflow test_bowtie2_align_single_end_large_index {
     input = [
         [ id:'test', single_end:true ], // meta map