From 2f675fbe7c60a67649dd4a02e72e2f1ee79f24d3 Mon Sep 17 00:00:00 2001
From: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Date: Tue, 16 Mar 2021 11:37:06 +0000
Subject: [PATCH] hifiasm tests init from fastqc

---
 tests/software/hifiasm/main.nf  | 28 ++++++++++++++++++++++++++++
 tests/software/hifiasm/test.yml | 19 +++++++++++++++++++
 2 files changed, 47 insertions(+)
 create mode 100644 tests/software/hifiasm/main.nf
 create mode 100644 tests/software/hifiasm/test.yml

diff --git a/tests/software/hifiasm/main.nf b/tests/software/hifiasm/main.nf
new file mode 100644
index 00000000..f10b2357
--- /dev/null
+++ b/tests/software/hifiasm/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTQC } from '../../../software/fastqc/main.nf' addParams( options: [:] )
+
+/*
+ * Test with single-end data
+ */
+workflow test_fastqc_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
+    FASTQC ( input )
+}
+
+/*
+ * Test with paired-end data
+ */
+workflow test_fastqc_paired_end {
+
+    def input = []
+    input = [[id: 'test', single_end: false], // meta map
+             [file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
+              file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true)]]
+    FASTQC (input)
+}
diff --git a/tests/software/hifiasm/test.yml b/tests/software/hifiasm/test.yml
new file mode 100644
index 00000000..0fe0ebe0
--- /dev/null
+++ b/tests/software/hifiasm/test.yml
@@ -0,0 +1,19 @@
+- name: fastqc single-end
+  command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config
+  tags:
+    - fastqc
+    - fastqc_single_end
+  files:
+    - path: ./output/fastqc/test_fastqc.html
+    - path: ./output/fastqc/test_fastqc.zip
+
+- name: fastqc paired-end
+  command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config
+  tags:
+    - fastqc
+    - fastqc_paired_end
+  files:
+    - path: ./output/fastqc/test_1_fastqc.html
+    - path: ./output/fastqc/test_2_fastqc.html
+    - path: ./output/fastqc/test_2_fastqc.zip
+    - path: ./output/fastqc/test_1_fastqc.zip