From b43c1f3937c1b1f25644c06e3efa1aa050576e52 Mon Sep 17 00:00:00 2001
From: Abhinav Sharma <abhi18av@gmail.com>
Date: Tue, 1 Dec 2020 12:19:52 +0530
Subject: [PATCH] Refactor the multiqc test code

---
 software/multiqc/test/main.nf         | 25 -------------------------
 software/multiqc/test/nextflow.config | 20 --------------------
 tests/software/multiqc/main.nf        | 19 +++++++++++++++++++
 tests/software/multiqc/test.yml       |  9 +++++++++
 4 files changed, 28 insertions(+), 45 deletions(-)
 delete mode 100755 software/multiqc/test/main.nf
 delete mode 100644 software/multiqc/test/nextflow.config
 create mode 100644 tests/software/multiqc/main.nf
 create mode 100644 tests/software/multiqc/test.yml

diff --git a/software/multiqc/test/main.nf b/software/multiqc/test/main.nf
deleted file mode 100755
index 60c7e1a0..00000000
--- a/software/multiqc/test/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MULTIQC } from '../main.nf'  addParams( options: [ publish_dir:'test_multi' ] )
-
-/*
- * Test with single-end data
- */
-workflow test_multi {
-
-    def input = []
-    input = [
-        file("${baseDir}/input/test_1_fastqc.html", checkIfExists: true),
-        file("${baseDir}/input/test_2_fastqc.html", checkIfExists: true),
-        file("${baseDir}/input/test_1_fastqc.zip", checkIfExists: true),
-        file("${baseDir}/input/test_2_fastqc.zip", checkIfExists: true)
-    ]
-
-    MULTIQC ( input )
-}
-
-workflow {
-    test_multi()
-}
diff --git a/software/multiqc/test/nextflow.config b/software/multiqc/test/nextflow.config
deleted file mode 100644
index 4149feea..00000000
--- a/software/multiqc/test/nextflow.config
+++ /dev/null
@@ -1,20 +0,0 @@
-
-params {
-    outdir = "output/"
-    publish_dir_mode = "copy"
-    enable_conda = false
-}
-
-profiles {
-    conda  {
-        params.enable_conda = true
-    }
-    docker {
-        docker.enabled = true
-        docker.runOptions = '-u \$(id -u):\$(id -g)'
-    }
-    singularity {
-        singularity.enabled = true
-        singularity.autoMounts = true
-    }
-}
diff --git a/tests/software/multiqc/main.nf b/tests/software/multiqc/main.nf
new file mode 100644
index 00000000..54fb78ed
--- /dev/null
+++ b/tests/software/multiqc/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MULTIQC } from '../../../software/multiqc/main.nf' addParams(options: [publish_dir: 'test_multiqc'])
+
+
+workflow test_multiqc {
+
+    def input = []
+
+    input = [[id: 'test'], // meta map
+             [file("${launchDir}/tests/data/fastqc/test_1.fastq.html", checkIfExists: true),
+              file("${launchDir}/tests/data/fastqc/test_1.fastq.zip", checkIfExists: true),
+              file("${launchDir}/tests/data/fastqc/test_2.fastq.html", checkIfExists: true),
+              file("${launchDir}/tests/data/fastqc/test_2.fastq.zip", checkIfExists: true)]]
+
+    MULTIQC(input)
+}
diff --git a/tests/software/multiqc/test.yml b/tests/software/multiqc/test.yml
new file mode 100644
index 00000000..664b524e
--- /dev/null
+++ b/tests/software/multiqc/test.yml
@@ -0,0 +1,9 @@
+- name: Run multiqc test workflow
+  command: nextflow run ./tests/software/multiqc/ -profile docker -entry test_multiqc -c tests/config/nextflow.config
+  tags:
+    - multiqc
+  files:
+    - path: output/test_multiqc/test_fastqc.html
+      md5sum: 7027e72c3e55292c1567f12e02565e3b
+    - path: output/test_multiqc/test_fastqc.html
+      md5sum: 7027e72c3e55292c1567f12e02565e3b