From 0a7b366f6f3fead1de89698ffa68a841a102352e Mon Sep 17 00:00:00 2001
From: lgrochowalski <lukasz.grochowalski@gmail.com>
Date: Mon, 18 Mar 2024 16:29:29 +0100
Subject: [PATCH] port htseq count pytest to nf-test (#5194)

* port htseq count pytest to nf-test

* rename yml file

* add extra line

* fix tag.yml

* fix meta.yml

* fix meta.yml

---------

Co-authored-by: zxBIB Grochowalski,Lukasz (GCBDS) EXTERNAL <lukasz.grochowalski.ext@boehringer-ingelheim.com>
Co-authored-by: Mauro Saporita <64437596+mauro-saporita@users.noreply.github.com>
---
 modules/nf-core/htseq/count/meta.yml          |  2 +-
 .../nf-core/htseq/count/tests/main.nf.test    | 72 +++++++++++++++++++
 .../htseq/count/tests/main.nf.test.snap       | 72 +++++++++++++++++++
 modules/nf-core/htseq/count/tests/tags.yml    |  2 +
 tests/config/pytest_modules.yml               |  3 -
 5 files changed, 147 insertions(+), 4 deletions(-)
 create mode 100644 modules/nf-core/htseq/count/tests/main.nf.test
 create mode 100644 modules/nf-core/htseq/count/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/htseq/count/tests/tags.yml

diff --git a/modules/nf-core/htseq/count/meta.yml b/modules/nf-core/htseq/count/meta.yml
index 1a036ffa3c0..9373e680e02 100644
--- a/modules/nf-core/htseq/count/meta.yml
+++ b/modules/nf-core/htseq/count/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://htseq.readthedocs.io/en/latest/"
       documentation: "https://htseq.readthedocs.io/en/latest/index.html"
       doi: "10.1093/bioinformatics/btu638"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/htseq/count/tests/main.nf.test b/modules/nf-core/htseq/count/tests/main.nf.test
new file mode 100644
index 00000000000..511c8d67f0d
--- /dev/null
+++ b/modules/nf-core/htseq/count/tests/main.nf.test
@@ -0,0 +1,72 @@
+nextflow_process {
+
+    name "Test Process HTSEQ_COUNT"
+    script "../main.nf"
+    process "HTSEQ_COUNT"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "htseq"
+    tag "htseq/count"
+
+    test("bam input") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+
+                ]
+                input[1] = [
+                    [ id:'test2'], // meta map
+                    file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.txt.get(0).get(1) ==~ ".*.txt" },
+                { assert snapshot(process.out).match() }
+            )
+            
+        }
+
+    }
+
+    test("cram input") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+
+                ]
+                input[1] = [
+                    [ id:'test2'], // meta map
+                    file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.txt.get(0).get(1) ==~ ".*.txt" },
+                { assert snapshot(process.out).match() }
+            )
+            
+        }
+
+    }
+
+
+}
diff --git a/modules/nf-core/htseq/count/tests/main.nf.test.snap b/modules/nf-core/htseq/count/tests/main.nf.test.snap
new file mode 100644
index 00000000000..e561310de7e
--- /dev/null
+++ b/modules/nf-core/htseq/count/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "bam input": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,5e37b2292f1d21945acb532afa5eb615"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4aad47e2b62180da87cd22e49b2cb1d6"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,5e37b2292f1d21945acb532afa5eb615"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4aad47e2b62180da87cd22e49b2cb1d6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T15:02:21.074352"
+    },
+    "cram input": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,53f9b007bd72115e8b72a40f859bc896"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4aad47e2b62180da87cd22e49b2cb1d6"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,53f9b007bd72115e8b72a40f859bc896"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4aad47e2b62180da87cd22e49b2cb1d6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T15:02:30.977775"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/htseq/count/tests/tags.yml b/modules/nf-core/htseq/count/tests/tags.yml
new file mode 100644
index 00000000000..232a7e55162
--- /dev/null
+++ b/modules/nf-core/htseq/count/tests/tags.yml
@@ -0,0 +1,2 @@
+htseq/count:
+  - "modules/nf-core/htseq/count/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 4794bf6a27c..6ddc580ab6f 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1046,9 +1046,6 @@ homer/pos2bed:
 hpsuissero:
   - modules/nf-core/hpsuissero/**
   - tests/modules/nf-core/hpsuissero/**
-htseq/count:
-  - modules/nf-core/htseq/count/**
-  - tests/modules/nf-core/htseq/count/**
 hypo:
   - modules/nf-core/hypo/**
   - tests/modules/nf-core/hypo/**