From a43bc940d6aaeaa755b34484cffeb5b41bce92eb Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Mon, 9 May 2022 11:15:14 +0000
Subject: [PATCH] Add suggestions from code review

---
 modules/meryl/count/meta.yml       |  1 +
 tests/modules/meryl/count/main.nf  | 17 +++++++++++++++--
 tests/modules/meryl/count/test.yml | 17 +++++++++++++----
 3 files changed, 29 insertions(+), 6 deletions(-)

diff --git a/modules/meryl/count/meta.yml b/modules/meryl/count/meta.yml
index dd59decd..854f8759 100644
--- a/modules/meryl/count/meta.yml
+++ b/modules/meryl/count/meta.yml
@@ -37,6 +37,7 @@ output:
   - meryl_db:
       type: directory
       description: A Meryl k-mer database
+      pattern: "*.meryldb"
 
 authors:
   - "@mahesh-panchal"
diff --git a/tests/modules/meryl/count/main.nf b/tests/modules/meryl/count/main.nf
index 7d65b7dd..3c9a64c7 100644
--- a/tests/modules/meryl/count/main.nf
+++ b/tests/modules/meryl/count/main.nf
@@ -4,12 +4,25 @@ nextflow.enable.dsl = 2
 
 include { MERYL_COUNT } from '../../../../modules/meryl/count/main.nf'
 
-workflow test_meryl_count {
+workflow test_meryl_count_single_end {
 
     input = [
-        [ id:'test' ], // meta map
+        [ id:'test' , single_end: true ], // meta map
         file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
     ]
 
     MERYL_COUNT ( input )
 }
+
+workflow test_meryl_count_paired_end {
+
+    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)
+        ]
+    ]
+
+    MERYL_COUNT ( input )
+}
diff --git a/tests/modules/meryl/count/test.yml b/tests/modules/meryl/count/test.yml
index 5437966c..6291a62f 100644
--- a/tests/modules/meryl/count/test.yml
+++ b/tests/modules/meryl/count/test.yml
@@ -1,8 +1,17 @@
-- name: meryl count test_meryl_count
-  command: nextflow run tests/modules/meryl/count -entry test_meryl_count -c tests/config/nextflow.config
+- name: meryl count test_meryl_count_single_end
+  command: nextflow run tests/modules/meryl/count -entry test_meryl_count_single_end -c tests/config/nextflow.config
   tags:
-    - meryl
     - meryl/count
+    - meryl
   files:
     - path: output/meryl/versions.yml
-      md5sum: 9bc9470c2eff996026781d5ff8c2b369
+      md5sum: 5fe537d873925ccbcc4edf0983e9eda0
+
+- name: meryl count test_meryl_count_paired_end
+  command: nextflow run tests/modules/meryl/count -entry test_meryl_count_paired_end -c tests/config/nextflow.config
+  tags:
+    - meryl/count
+    - meryl
+  files:
+    - path: output/meryl/versions.yml
+      md5sum: 4961f13cfb60ba8764ed666e70dbf12c