From 8a19929d03832ecaf95a50962898882de04e6884 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 3 May 2024 09:50:42 +0200
Subject: [PATCH] Set up tests

---
 .gitignore                           |  1 +
 nf-test.config                       |  8 ++++++++
 tests/main.nf.test                   | 20 +++++++++++++++++++
 tests/nextflow.config                |  5 +++++
 tests/workflows/seqinspector.nf.test | 30 ++++++++++++++++++++++++++++
 5 files changed, 64 insertions(+)
 create mode 100644 nf-test.config
 create mode 100644 tests/main.nf.test
 create mode 100644 tests/nextflow.config
 create mode 100644 tests/workflows/seqinspector.nf.test

diff --git a/.gitignore b/.gitignore
index 5124c9a..089a407 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test
diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 0000000..6969c08
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    profile "test,docker"
+
+}
diff --git a/tests/main.nf.test b/tests/main.nf.test
new file mode 100644
index 0000000..72498b5
--- /dev/null
+++ b/tests/main.nf.test
@@ -0,0 +1,20 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "tests/results"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 0000000..c19b1ad
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1,5 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
diff --git a/tests/workflows/seqinspector.nf.test b/tests/workflows/seqinspector.nf.test
new file mode 100644
index 0000000..bbb529d
--- /dev/null
+++ b/tests/workflows/seqinspector.nf.test
@@ -0,0 +1,30 @@
+nextflow_workflow {
+
+    name "Test Workflow SEQINSPECTOR"
+    script "workflows/seqinspector.nf"
+    workflow "SEQINSPECTOR"
+
+    test("Should run without failures pipeline") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                // outdir = "tests/results"
+            }
+            workflow {
+                """
+                // define inputs of the workflow here. Example:
+                // input[0] = file("https://raw.githubusercontent.com/nf-core/test-datasets/e47966b63444ec0fcdef23bfc410eeca22535ac7/testdata/MiSeq/samplesheet.csv")
+                input[0] = file("assets/samplesheet.csv")
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+}