From 1ddc2821c7bc890907642c258955e4608aced0ed Mon Sep 17 00:00:00 2001
From: Emilio Palumbo <emiliopalumbo@gmail.com>
Date: Thu, 18 Apr 2024 18:55:36 +0200
Subject: [PATCH] Add nf-test for inferExp process

---
 tests/modules/inferExp/rseqc/main.nf.test     | 47 +++++++++++++++++++
 .../modules/inferExp/rseqc/main.nf.test.snap  | 38 +++++++++++++++
 2 files changed, 85 insertions(+)
 create mode 100644 tests/modules/inferExp/rseqc/main.nf.test
 create mode 100644 tests/modules/inferExp/rseqc/main.nf.test.snap

diff --git a/tests/modules/inferExp/rseqc/main.nf.test b/tests/modules/inferExp/rseqc/main.nf.test
new file mode 100644
index 0000000..fadaed9
--- /dev/null
+++ b/tests/modules/inferExp/rseqc/main.nf.test
@@ -0,0 +1,47 @@
+nextflow_process {
+
+    name "Test Process inferExp"
+    script "modules/inferExp/rseqc/main.nf"
+    process "inferExp"
+
+    test("Should infer strendedness from BAM (compressed annotation)") {
+
+        when {
+            process {
+                """
+                input[0] = file("${baseDir}/data/annotation.gtf.gz")
+                input[1] = Channel.from([
+                    [ "sample3", "test3", file("${baseDir}/data/sample3_m4_n10_toGenome.bam"), "bam", "GenomeAlignments", true]
+                ])
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+    test("Should infer strendedness from BAM (uncompressed annotation)") {
+
+        when {
+            process {
+                """
+                input[0] = file("${baseDir}/data/annotation.gtf.gz")
+                input[1] = Channel.from([
+                    [ "sample3", "test3", file("${baseDir}/data/sample3_m4_n10_toGenome.bam"), "bam", "GenomeAlignments", true]
+                ])
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}
diff --git a/tests/modules/inferExp/rseqc/main.nf.test.snap b/tests/modules/inferExp/rseqc/main.nf.test.snap
new file mode 100644
index 0000000..530680d
--- /dev/null
+++ b/tests/modules/inferExp/rseqc/main.nf.test.snap
@@ -0,0 +1,38 @@
+{
+    "Should infer strendedness from BAM (uncompressed annotation)": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "sample3",
+                        "test3",
+                        "{\"paired\": true, \"exp\": \"MATE2_SENSE\"}"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-18T18:54:10.824148"
+    },
+    "Should infer strendedness from BAM (compressed annotation)": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "sample3",
+                        "test3",
+                        "{\"paired\": true, \"exp\": \"MATE2_SENSE\"}"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-18T18:54:02.195879"
+    }
+}
\ No newline at end of file