Added nf-tests for ADAPTERREMOVALFIXPREFIX (#6243)

* Added nf-tests for ADAPTERREMOVALFIXPREFIX * Update modules/nf-core/adapterremovalfixprefix/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/adapterremovalfixprefix/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · Aug 22, 2024 · 5662e1d · 5662e1d
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diff --git a/modules/nf-core/adapterremovalfixprefix/tests/main.nf.test b/modules/nf-core/adapterremovalfixprefix/tests/main.nf.test
@@ -0,0 +1,72 @@
+nextflow_process {
+
+    name "Test Process ADAPTERREMOVALFIXPREFIX"
+    script "../main.nf"
+    process "ADAPTERREMOVALFIXPREFIX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "adapterremoval"
+    tag "adapterremovalfixprefix"
+
+    setup {
+        run("ADAPTERREMOVAL") {
+            script "../../adapterremoval/main.nf"
+            config "./nextflow.config"
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[1] = []
+                """
+            }
+        }
+    }
+
+    test("paired-end - sarscov2 - [fastq]") {
+
+        when {
+
+            process {
+                """
+                input[0] = ADAPTERREMOVAL.out.collapsed
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("paired-end - sarscov2 - [fastq] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = ADAPTERREMOVAL.out.collapsed
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/adapterremovalfixprefix/tests/main.nf.test.snap b/modules/nf-core/adapterremovalfixprefix/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "paired-end - sarscov2 - [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fq.gz:md5,369452751050a7f1e31b839702d61417"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,76647a727690a8fbafa77a4b77cbe64c"
+                ],
+                "fixed_fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fq.gz:md5,369452751050a7f1e31b839702d61417"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,76647a727690a8fbafa77a4b77cbe64c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T08:19:25.477451"
+    },
+    "paired-end - sarscov2 - [fastq]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fq.gz:md5,369452751050a7f1e31b839702d61417"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,76647a727690a8fbafa77a4b77cbe64c"
+                ],
+                "fixed_fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fq.gz:md5,369452751050a7f1e31b839702d61417"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,76647a727690a8fbafa77a4b77cbe64c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T07:57:53.853795"
+    }
+}
diff --git a/modules/nf-core/adapterremovalfixprefix/tests/nextflow.config b/modules/nf-core/adapterremovalfixprefix/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: ADAPTERREMOVAL {
+        ext.args = "--collapse"
+    }
+}
diff --git a/modules/nf-core/adapterremovalfixprefix/tests/tags.yml b/modules/nf-core/adapterremovalfixprefix/tests/tags.yml
@@ -0,0 +1,2 @@
+adapterremovalfixprefix:
+  - "modules/nf-core/adapterremovalfixprefix/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1,6 +1,3 @@
-adapterremovalfixprefix:
-  - modules/nf-core/adapterremovalfixprefix/**
-  - tests/modules/nf-core/adapterremovalfixprefix/**
 amps:
   - modules/nf-core/amps/**
   - tests/modules/nf-core/amps/**

diff --git a/tests/modules/nf-core/adapterremovalfixprefix/main.nf b/tests/modules/nf-core/adapterremovalfixprefix/main.nf
diff --git a/tests/modules/nf-core/adapterremovalfixprefix/nextflow.config b/tests/modules/nf-core/adapterremovalfixprefix/nextflow.config
diff --git a/tests/modules/nf-core/adapterremovalfixprefix/test.yml b/tests/modules/nf-core/adapterremovalfixprefix/test.yml