update and add topics to snakemake module (#9454)

* update and add topics

* add new topics structure

* add stub test and capture version in snapshot

* update to 9.14.0

* fix singularity be setting cache_dir

* fix stub

---------

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: mashehu <mashehu3@gmail.com>

Author: 2 people

modules/nf-core/snakemake/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::snakemake=7.31.0
+  - bioconda::snakemake=9.14.0

modules/nf-core/snakemake/main.nf

@@ -1,56 +1,51 @@
 process SNAKEMAKE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     // You will have to add all modules to this Conda definition and
     // replace the container definition for one that suits your needs
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/snakemake:7.31.0--hdfd78af_1' :
-        'biocontainers/snakemake:7.31.0--hdfd78af_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b91b2eddb4c4c0a5e17721d29764e59a50035b9fa9996eb9cb392829f2d7a533/data'
+        : 'community.wave.seqera.io/library/snakemake:9.14.0--dfee75b6201d25c6'}"
 
     input:
     tuple val(meta), path(inputs)
     tuple val(meta2), path(snakefile)
 
     output:
-    tuple val(meta), path("[!.snakemake|versions.yml]**")         , emit: outputs      , optional: true
+    tuple val(meta), path("[!.snakemake|versions.yml]**"), emit: outputs, optional: true
     tuple val(meta), path(".snakemake", type: 'dir', hidden: true), emit: snakemake_dir
-    path "versions.yml"                                           , emit: versions
+    tuple val("${task.process}"), val("snakemake"), eval('snakemake --version'), topic: versions, emit: versions_snakemake
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args   = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def cores  = task.cpus ? "--cores ${task.cpus}" : "--cores all"
+    def args = task.ext.args ?: ''
+    def cores = task.cpus ? "--cores ${task.cpus}" : "--cores all"
     """
+    export XDG_CACHE_HOME=\$PWD/snakemake_cache
+    mkdir -p \$XDG_CACHE_HOME
+
     snakemake \\
-        $args \\
-        $cores \\
-        --snakefile $snakefile
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        snakemake: \$(snakemake --version)
-    END_VERSIONS
+        ${args} \\
+        ${cores} \\
+        --snakefile ${snakefile}
     """
 
+
     stub:
-    def args   = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def cores  = task.cpus ? "--cores ${task.cpus}" : "--cores all"
+    def args = task.ext.args ?: ''
+    def cores = task.cpus ? "--cores ${task.cpus}" : "--cores all"
     """
+    export XDG_CACHE_HOME=\$PWD/snakemake_cache
+    mkdir -p \$XDG_CACHE_HOME
+
     snakemake \\
-        $args \\
-        --snakefile $snakefile \\
-        $cores \\
+        ${args} \\
+        --snakefile ${snakefile} \\
+        ${cores} \\
         --dry-run
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        snakemake: \$(snakemake --version)
-    END_VERSIONS
     """
 }

modules/nf-core/snakemake/meta.yml

@@ -1,8 +1,7 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "snakemake"
-description: The Snakemake workflow management system is a tool to create reproducible
-  and scalable data analyses. This module runs a simple Snakemake pipeline based on
-  input snakefile. Expect many limitations."
+description: The Snakemake workflow management system is a tool to create
+  reproducible and scalable data analyses. This module runs a simple Snakemake
+  pipeline based on input snakefile. Expect many limitations."
 keywords:
   - snakemake
   - workflow
@@ -39,7 +38,6 @@ input:
           Snakefile to use with Snakemake. This is required for proper execution of Snakemake.
         ontologies: []
 output:
-  #Only when we have meta
   outputs:
     - - meta:
           type: map
@@ -59,16 +57,31 @@ output:
             e.g. [ id:'test', single_end:false ]
       - .snakemake:
           type: directory
-          description: Hidden directory containing Snakemake execution logs and metadata
+          description: Hidden directory containing Snakemake execution logs and
+            metadata
           pattern: ".snakemake"
           ontologies: []
+  versions_snakemake:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - snakemake:
+          type: string
+          description: The name of the tool
+      - "snakemake --version":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - snakemake:
+          type: string
+          description: The name of the tool
+      - "snakemake --version":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@adamrtalbot"
 maintainers:

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

@@ -18,7 +18,7 @@ nextflow_process {
             []
         ]
 // Snakefile
-    Channel.of('''
+    channel.of('''
 rule all:
     input: "hello.txt"
 
@@ -42,12 +42,57 @@ rule hello_world:
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.outputs, process.out.versions).match() }
+                { assert snapshot(
+                    process.out.outputs,
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
             )
         }
-
     }
+    test("Should run without failures - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+        // Input file
+        input[0] = [
+            [ id: 'input'],
+            []
+        ]
+// Snakefile
+    channel.of('''
+rule all:
+    input: "hello.txt"
+
+rule hello_world:
+    output: "hello.txt"
+    shell: "echo Hello World > hello.txt"
+
+'''
+        )
+        .collectFile(name: 'Snakefile')
+        .map { file ->
+            [
+                [id: 'Snakefile'],
+                file
+            ]}
+        .set{ snakefile }
+
+        input[1] = snakefile
+                """
+            }
+        }
 
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out.outputs,
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
+            )
+        }
+    }
 }

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

@@ -1,4 +1,25 @@
 {
+    "Should run without failures - stub": {
+        "content": [
+            [
+                
+            ],
+            {
+                "versions_snakemake": [
+                    [
+                        "SNAKEMAKE",
+                        "snakemake",
+                        "9.14.0"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-28T17:17:18.329663"
+    },
     "Should run without failures": {
         "content": [
             [
@@ -9,10 +30,20 @@
                     "hello.txt:md5,e59ff97941044f85df5297e1c302d260"
                 ]
             ],
-            [
-                "versions.yml:md5,91f038cba572e2b7b6dfe06e0e088ce5"
-            ]
+            {
+                "versions_snakemake": [
+                    [
+                        "SNAKEMAKE",
+                        "snakemake",
+                        "9.14.0"
+                    ]
+                ]
+            }
         ],
-        "timestamp": "2023-08-17T14:14:11+0000"
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-28T17:17:01.780244"
     }
 }