try porting mmseqs/search to nf-test

modules/nf-core/mmseqs/search/main.nf

@@ -1,4 +1,3 @@
-
 process MMSEQS_SEARCH {
     tag "$meta.id"
     label 'process_high'
@@ -13,7 +12,7 @@ process MMSEQS_SEARCH {
     tuple val(meta2), path(db_target)
 
     output:
-    tuple val(meta), path("${prefix}"), emit: db_search
+    tuple val(meta), path("${prefix}/"), emit: db_search
     path "versions.yml"               , emit: versions
 
     when:
@@ -51,8 +50,7 @@ process MMSEQS_SEARCH {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     if ("$db_query" == "${prefix}" || "$db_target" == "${prefix}"  ) error "Input and output names of databases are the same, set prefix in module configuration to disambiguate!"
     """
     mkdir -p $prefix

modules/nf-core/mmseqs/search/tests/main.nf.test

@@ -0,0 +1,89 @@
+nextflow_process {
+
+    name "Test Process MMSEQS_SEARCH"
+    script "../main.nf"
+    process "MMSEQS_SEARCH"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "mmseqs"
+    tag "mmseqs/search"
+    tag "mmseqs/createdb"
+
+    setup {
+        run("MMSEQS_CREATEDB", alias: "MMSEQS_CREATEDB_QUERY") {
+            script "../../../mmseqs/createdb/main.nf"
+            process {
+                """
+                input[0] = [ [ id:'test_query', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        run("MMSEQS_CREATEDB", alias: "MMSEQS_CREATEDB_TARGET") {
+            script ".../../../mmseqs/createdb/main.nf"
+            process {
+                """
+                input[0] = [ [ id:'test_target', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - test-search") {
+
+        when {
+            params {
+                module_args   = '--remove-tmp-files 1 --search-type 2'
+                module_prefix = 'test_output_search'
+            }
+            process {
+                """
+                input[0] = MMSEQS_CREATEDB_QUERY.out.db,
+                input[1] = MMSEQS_CREATEDB_TARGET.out.db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - test-search - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = MMSEQS_CREATEDB_QUERY.out.db,
+                input[1] = MMSEQS_CREATEDB_TARGET.out.db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                    ).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/mmseqs/search/tests/nextflow.config

@@ -0,0 +1,8 @@
+process {
+
+    withName: MMSEQS_SEARCH {
+        ext.prefix = module_prefix
+        ext.args = params.module_args
+    }
+
+}

tests/config/pytest_modules.yml

@@ -350,9 +350,6 @@ mitohifi/mitohifi:
 mmseqs/easysearch:
   - modules/nf-core/mmseqs/easysearch/**
   - tests/modules/nf-core/mmseqs/easysearch/**
-mmseqs/search:
-  - modules/nf-core/mmseqs/search/**
-  - tests/modules/nf-core/mmseqs/search/**
 mmseqs/tsv2exprofiledb:
   - modules/nf-core/mmseqs/tsv2exprofiledb/**
   - tests/modules/nf-core/mmseqs/tsv2exprofiledb/**