Migrate authentict/deam2cont to nf-test

modules/nf-core/authentict/deam2cont/environment.yml

@@ -5,3 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::authentict=1.0.1
+  - bioconda::samtools=1.16.1

modules/nf-core/authentict/deam2cont/main.nf

@@ -41,4 +41,16 @@ process AUTHENTICT_DEAM2CONT {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub :
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        authentict: \$(echo \$(AuthentiCT --version 2>&1) )
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

modules/nf-core/authentict/deam2cont/tests/main.nf.test

@@ -0,0 +1,75 @@
+nextflow_process {
+
+    name "Test Process AUTHENTICT_DEAM2CONT"
+
+    script "../main.nf"
+    process "AUTHENTICT_DEAM2CONT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "authentict"
+    tag "authentict/deam2cont"
+    tag "samtools"
+    tag "samtools/calmd"
+
+    setup {
+        run("SAMTOOLS_CALMD") {
+            script "../../../samtools/calmd/main.nf"
+
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],// meta map
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam",checkIfExists:true)
+                ]
+                input[1] = [
+                    [id : "genome"],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta",checkIfExists:true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("test_authentict_deam2cont") {
+        when {
+            process {
+                """
+                input[0] = SAMTOOLS_CALMD.out.bam
+                input[1] = [[],[]]
+                input[2] = [[],[]]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_authentict_deam2cont - stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = SAMTOOLS_CALMD.out.bam
+                input[1] = [[],[]]
+                input[2] = [[],[]]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    process.out.versions.collect{path(it).yaml}
+                ).match() }
+            )
+        }
+    }
+}

modules/nf-core/authentict/deam2cont/tests/main.nf.test.snap

@@ -0,0 +1,80 @@
+{
+    "test_authentict_deam2cont - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,961ace1ec9622bad5cf075b76410bdd2"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,961ace1ec9622bad5cf075b76410bdd2"
+                ]
+            },
+            [
+                {
+                    "AUTHENTICT_DEAM2CONT": {
+                        "authentict": "1.0.1",
+                        "samtools": "1.16.1"
+                    }
+                }
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-24T11:23:39.766851518"
+    },
+    "test_authentict_deam2cont": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,ab81cf4fbb7eedea260798c5bcad6a5d"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,961ace1ec9622bad5cf075b76410bdd2"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,ab81cf4fbb7eedea260798c5bcad6a5d"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,961ace1ec9622bad5cf075b76410bdd2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-24T11:23:30.499727901"
+    }
+}

tests/config/pytest_modules.yml

@@ -1,6 +1,3 @@
-authentict/deam2cont:
-  - modules/nf-core/authentict/deam2cont/**
-  - tests/modules/nf-core/authentict/deam2cont/**
 bamtools/convert:
   - modules/nf-core/bamtools/convert/**
   - tests/modules/nf-core/bamtools/convert/**