try porting mmseqs/search to nf-test (#7231)

* try porting to nf-test * remove from pytest * Apply suggestions from code review Co-authored-by: Jim Downie <[email protected]> * fix stub * remove pytest * Working except for linting * Only check the names * Fix meta for linting --------- Co-authored-by: Jim Downie <[email protected]> Co-authored-by: Simon Pearce <[email protected]>
nf-core · Jan 15, 2025 · 0853f51 · 0853f51
1 parent 89a5ca7
commit 0853f51
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Showing 10 changed files with 199 additions and 69 deletions.
diff --git a/modules/nf-core/mmseqs/easysearch/main.nf b/modules/nf-core/mmseqs/easysearch/main.nf
@@ -47,11 +47,8 @@ process MMSEQS_EASYSEARCH {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: "*.dbtype"
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    ${prefix}.tsv
+    touch ${prefix}.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/mmseqs/search/main.nf b/modules/nf-core/mmseqs/search/main.nf
@@ -1,19 +1,18 @@
-
 process MMSEQS_SEARCH {
     tag "$meta.id"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:14.7e284--pl5321h6a68c12_2':
-        'biocontainers/mmseqs2:14.7e284--pl5321h6a68c12_2' }"
+        'https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_0':
+        'biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_0' }"
 
     input:
     tuple val(meta), path(db_query)
     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:
@@ -40,9 +39,7 @@ process MMSEQS_SEARCH {
         ${prefix}/${prefix} \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
-
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -51,8 +48,7 @@ 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
@@ -62,7 +58,7 @@ process MMSEQS_SEARCH {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        mmseqs: \$(mmseqs | grep 'Version' | sed 's/MMseqs2 Version: /')
+        mmseqs: \$(mmseqs | grep 'Version' | sed 's/MMseqs2 Version: //')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/mmseqs/search/meta.yml b/modules/nf-core/mmseqs/search/meta.yml
@@ -43,7 +43,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'test', single_end:false ]`
-      - ${prefix}:
+      - ${prefix}/:
           type: directory
           description: an MMseqs2 database with search results
   - versions:

diff --git a/modules/nf-core/mmseqs/search/tests/main.nf.test b/modules/nf-core/mmseqs/search/tests/main.nf.test
@@ -0,0 +1,95 @@
+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"
+
+    config "./nextflow.config"
+
+    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.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/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.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/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(
+                    file(process.out.db_search.get(0).get(1)).list().sort(), //second file is empty so fails linting
+                    path(process.out.versions[0]).yaml
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - test-search - stub") {
+
+        options "-stub"
+
+        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() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/mmseqs/search/tests/main.nf.test.snap b/modules/nf-core/mmseqs/search/tests/main.nf.test.snap
@@ -0,0 +1,88 @@
+{
+    "sarscov2 - test-search": {
+        "content": [
+            [
+                "test_output_search.0",
+                "test_output_search.1",
+                "test_output_search.dbtype",
+                "test_output_search.index"
+            ],
+            {
+                "MMSEQS_SEARCH": {
+                    "mmseqs": "15.6f452"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-15T09:38:30.159081322"
+    },
+    "sarscov2 - test-search - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_query",
+                            "single_end": true
+                        },
+                        [
+                            "test_output_search.0:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.1:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.3:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.4:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.5:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.6:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.7:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.8:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.9:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.index:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2568126b1f8eb47999b31cd5f3b9c68e"
+                ],
+                "db_search": [
+                    [
+                        {
+                            "id": "test_query",
+                            "single_end": true
+                        },
+                        [
+                            "test_output_search.0:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.1:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.3:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.4:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.5:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.6:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.7:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.8:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.9:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_output_search.index:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2568126b1f8eb47999b31cd5f3b9c68e"
+                ]
+            },
+            {
+                "MMSEQS_SEARCH": {
+                    "mmseqs": "15.6f452"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-15T09:28:46.406630911"
+    }
+}
diff --git a/modules/nf-core/mmseqs/search/tests/nextflow.config b/modules/nf-core/mmseqs/search/tests/nextflow.config
@@ -0,0 +1,8 @@
+process {
+
+    withName: MMSEQS_SEARCH {
+        ext.prefix = params.module_prefix
+        ext.args = params.module_args
+    }
+
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -323,9 +323,6 @@ 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/**

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