Added nf-test for gfaffix

modules/nf-core/gfaffix/environment.yml

@@ -2,6 +2,5 @@ name: gfaffix
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::gfaffix=0.1.5
+  - bioconda::gfaffix=0.1.5b

modules/nf-core/gfaffix/main.nf

@@ -30,7 +30,19 @@ process GFAFFIX {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        gfaffix: \$(gfaffix --version 2>&1 | grep -o 'gfaffix .*' | cut -f2 -d ' ')
+        gfaffix: \$(gfaffix --version | grep -o 'gfaffix .*' | cut -f2 -d ' ')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.gfaffix.gfa
+    touch ${prefix}.affixes.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gfaffix: \$(gfaffix --version | grep -o 'gfaffix .*' | cut -f2 -d ' ')
     END_VERSIONS
     """
 }

modules/nf-core/gfaffix/tests/main.nf.test

@@ -0,0 +1,63 @@
+
+nextflow_process {
+
+    name "Test Process GFAFFIX"
+    script "../main.nf"
+    process "GFAFFIX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gfaffix"
+
+    test("test-gfaffix") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+				    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.gfa,
+                    process.out.affixes,
+                    process.out.versions,
+                    file(process.out.versions[0]).readLines().collect { it.trim() }, // Trap for conda version mismatches
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-gfaffix-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+				    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/gfaffix/tests/main.nf.test.snap

@@ -0,0 +1,83 @@
+{
+    "test-gfaffix": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gfaffix.gfa:md5,30d7a68fc07623779dbb3d708320c844"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.affixes.txt:md5,c3540baa386462552d7ebe4e4b7eda6a"
+                ]
+            ],
+            [
+                "versions.yml:md5,3ec7c6a9cbafbb8131f4e325e140aa80"
+            ],
+            [
+                "\"GFAFFIX\":",
+                "gfaffix: 0.1.5b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T14:14:01.340269"
+    },
+    "test-gfaffix-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gfaffix.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.affixes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,3ec7c6a9cbafbb8131f4e325e140aa80"
+                ],
+                "affixes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.affixes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "gfa": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gfaffix.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3ec7c6a9cbafbb8131f4e325e140aa80"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T14:36:34.068923"
+    }
+}

tests/config/pytest_modules.yml

@@ -269,9 +269,6 @@ genrich:
 geoquery/getgeo:
   - modules/nf-core/geoquery/getgeo/**
   - tests/modules/nf-core/geoquery/getgeo/**
-gfaffix:
-  - modules/nf-core/gfaffix/**
-  - tests/modules/nf-core/gfaffix/**
 gfastats:
   - modules/nf-core/gfastats/**
   - tests/modules/nf-core/gfastats/**