From 84c0bda00e46a356c5eae852a6c8a3f9b64865fc Mon Sep 17 00:00:00 2001
From: Abhinav Sharma <abhi18av@users.noreply.github.com>
Date: Thu, 3 Dec 2020 09:42:34 +0530
Subject: [PATCH] Apply suggestions from code review by @Emiller88

---
 tests/software/fastqc/main.nf  | 13 +++++++++----
 tests/software/multiqc/main.nf | 14 ++++++--------
 2 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/tests/software/fastqc/main.nf b/tests/software/fastqc/main.nf
index 597d56f6..7885c903 100644
--- a/tests/software/fastqc/main.nf
+++ b/tests/software/fastqc/main.nf
@@ -23,9 +23,14 @@ workflow test_single_end {
 workflow test_paired_end {
 
     def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
+    input = [[id: 'test', single_end: false], // meta map
+             [file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+              file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true)]]
+
+    FASTQC_PE(input)
+
+    emit:
+    html = FASTQC_PE.out.html
+    zip = FASTQC_PE.out.zip
 
-    FASTQC_PE ( input )
 }
diff --git a/tests/software/multiqc/main.nf b/tests/software/multiqc/main.nf
index 9ff15f27..a6ff0082 100644
--- a/tests/software/multiqc/main.nf
+++ b/tests/software/multiqc/main.nf
@@ -3,17 +3,15 @@
 nextflow.enable.dsl = 2
 
 include { MULTIQC } from '../../../software/multiqc/main.nf' addParams(options: [publish_dir: 'test_multiqc'])
-
+include { test_paired_end } from '../fastqc/main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
 
 workflow test_multiqc {
+    test_paired_end()
 
-    def input = []
-
-    input = [[id: 'test'], // meta map
-             [file("${launchDir}/tests/data/fastqc/test_1_fastqc.html", checkIfExists: true),
-              file("${launchDir}/tests/data/fastqc/test_1_fastqc.zip", checkIfExists: true),
-              file("${launchDir}/tests/data/fastqc/test_2_fastqc.html", checkIfExists: true),
-              file("${launchDir}/tests/data/fastqc/test_2_fastqc.zip", checkIfExists: true)]]
+    input = [
+        [id: 'test'],
+        test_paired_end.out.html.join(test_paired_end.out.zip, by: 0).flatten().filter(java.nio.file.Path).toList()
+    ]
 
     MULTIQC(input)
 }