Update stub test for interproscan

Author: olgabot

subworkflows/local/interproscan/main.nf

@@ -41,9 +41,9 @@ workflow INTERPROSCAN {
     ch_versions = ch_versions.mix(INTERPROSCAN_RUN.out.versions.first())
 
     emit:
-    tsv = INTERPROSCAN_RUN.out.tsv // channel: [ val(meta), [ tsv ] ]
-    xml = INTERPROSCAN_RUN.out.xml // channel: [ val(meta), [ xml ] ]
     gff3 = INTERPROSCAN_RUN.out.gff3 // channel: [ val(meta), [ gff3 ] ]
     json = INTERPROSCAN_RUN.out.json // channel: [ val(meta), [ json ] ]
+    tsv = INTERPROSCAN_RUN.out.tsv // channel: [ val(meta), [ tsv ] ]
+    xml = INTERPROSCAN_RUN.out.xml // channel: [ val(meta), [ xml ] ]
     versions = ch_versions // channel: [ versions.yml ]
 }

subworkflows/local/interproscan/tests/main.nf.test

@@ -14,13 +14,13 @@ nextflow_workflow {
     tag "untar"
 
 
-    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
     test("interproscan -- input: tar.gz, untar") {
 
         when {
             params {
                 interproscan_tar_gz = "${moduleTestDir}/fixtures/interproscan-5.73-104.0.tar.gz"
                 interproscan_database_version = "interproscan-5.73-104.0"
+                outdir = "results/"
             }
             workflow {
                 """
@@ -46,4 +46,49 @@ nextflow_workflow {
             )
         }
     }
+
+    test("interproscan -- input: tar.gz, untar -- stub") {
+        tag "stub"
+        tag "CI"
+        options "-stub"
+
+        when {
+            params {
+                interproscan_tar_gz = "${moduleTestDir}/fixtures/interproscan-5.73-104.0.tar.gz"
+                interproscan_database_version = "interproscan-5.73-104.0"
+                outdir = "results/"
+            }
+            workflow {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id:'test1', single_end:false ], // meta map
+                        file("${moduleTestDir}/fixtures/test1.fasta", checkIfExists: true)
+                    ],
+                    [
+                        [ id:'test2', single_end:false ], // meta map
+                        file("${moduleTestDir}/fixtures/test2.fasta", checkIfExists: true)
+                    ]
+                )
+                """
+        }
+        }
+
+        then {
+            println "Number of output channels: ${workflow.out.size()}"
+            assertAll(
+                { assert workflow.success },
+                // Warning: all of the outputs MUST be in the same order as the emit: "directive(?)"
+                // We chose alphabetical sorting except for versions because you gotta pick some ordering
+                { assert snapshot(
+                    workflow.out.gff3,
+                    workflow.out.json,
+                    workflow.out.tsv,
+                    workflow.out.xml,
+                    workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
 }

subworkflows/local/interproscan/tests/main.nf.test.snap

@@ -1,43 +1,78 @@
 {
-    "interproscan -- input: tar.gz, untar": {
+    "interproscan -- input: tar.gz, untar -- stub": {
         "content": [
-            {
-                "0": [
-                    
+            [
+                [
+                    {
+                        "id": "test1",
+                        "single_end": false
+                    },
+                    "test1.gff3.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    
-                ],
-                "gff3": [
-                    
-                ],
-                "json": [
-                    
+                [
+                    {
+                        "id": "test2",
+                        "single_end": false
+                    },
+                    "test2.gff3.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test1",
+                        "single_end": false
+                    },
+                    "test1.json.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
-                "tsv": [
-                    
+                [
+                    {
+                        "id": "test2",
+                        "single_end": false
+                    },
+                    "test2.json.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test1",
+                        "single_end": false
+                    },
+                    "test1.tsv.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
-                "versions": [
-                    
+                [
+                    {
+                        "id": "test2",
+                        "single_end": false
+                    },
+                    "test2.tsv.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test1",
+                        "single_end": false
+                    },
+                    "test1.xml.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
-                "xml": [
-                    
+                [
+                    {
+                        "id": "test2",
+                        "single_end": false
+                    },
+                    "test2.xml.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
-            }
+            ],
+            [
+                "versions.yml:md5,448c213a3be7face5f23a2fe79622fb4"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.1"
         },
-        "timestamp": "2025-05-13T16:31:13.768834"
+        "timestamp": "2025-06-03T11:33:01.738065"
     }
 }