Assemblyscan 1.0.0

modules/nf-core/assemblyscan/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::assembly-scan=0.4.1
+  - bioconda::assembly-scan=1.0.0

modules/nf-core/assemblyscan/main.nf

@@ -4,27 +4,34 @@ process ASSEMBLYSCAN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0' :
-        'biocontainers/assembly-scan:0.4.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/assembly-scan:1.0.0--pyhdfd78af_0' :
+        'biocontainers/assembly-scan:1.0.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(assembly)
 
     output:
-    tuple val(meta), path("*.json"), emit: json
-    path "versions.yml"            , emit: versions
+    tuple val(meta), path("*.{json,tsv}"),     emit: report
+    tuple val("${task.process}"), val('assemblyscan'), eval("assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\$//'"), topic: versions, emit: versions_assemblyscan
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args        = task.ext.args   ?: ''
+    def prefix      = task.ext.prefix ?: "${meta.id}"
+    def file_format = (task.ext.args?.contains("--json")) ? "json" : "tsv"
+    """
+    assembly-scan \\
+         ${args} \\
+         ${assembly} > ${prefix}.${file_format}
     """
-    assembly-scan ${assembly} > ${prefix}.json
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        assemblyscan: \$( assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\$//' )
-    END_VERSIONS
+    stub:
+    def args        = task.ext.args   ?: ''
+    def prefix      = task.ext.prefix ?: "${meta.id}"
+    def file_format = (task.ext.args?.contains("--json")) ? "json" : "tsv"
+    """
+    touch ${prefix}.${file_format}
     """
 }

modules/nf-core/assemblyscan/meta.yml

@@ -25,28 +25,46 @@ input:
         pattern: "*.fasta"
         ontologies: []
 output:
-  json:
+  report:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.json":
+      - "*.{json,tsv}":
           type: file
-          description: Assembly statistics in JSON format
-          pattern: "*.json"
+          description: Assembly statistics in tsv or JSON format
+          pattern: "*.{json,tsv}"
           ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
             - edam: http://edamontology.org/format_3464 # JSON
+  versions_assemblyscan:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - assemblyscan:
+          type: string
+          description: The tool name
+      - "assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\\$//'":
+          type: string
+          description: The command used to generate 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
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - assemblyscan:
+          type: string
+          description: The tool name
+      - "assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\\$//'":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@sateeshperi"
   - "@mjcipriano"
+  - "@eit-maxlcummins"
+  - "@charles-plessy"
 maintainers:
   - "@sateeshperi"
   - "@mjcipriano"
+  - "@eit-maxlcummins"

modules/nf-core/assemblyscan/tests/json.config

@@ -0,0 +1,5 @@
+process {
+    withName: 'ASSEMBLYSCAN' {
+        ext.args = "--json"
+    }
+}

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

@@ -7,6 +7,27 @@ nextflow_process {
     tag "modules_nfcore"
     tag "assemblyscan"
 
+      test("genome.fasta - json") {
+
+        when {
+            config './json.config'
+            process {
+                """
+                input[0] =  [ [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
     test("genome.fasta") {
 
         when {
@@ -26,4 +47,25 @@ nextflow_process {
             )
         }
     }
+
+    test("genome.fasta - stub") {
+
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] =  [ [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }

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

@@ -8,26 +8,124 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.json:md5,9140e3d43f2d676f62e1325ace5dd8bd"
+                        "test.tsv:md5,d3bda95a4a6f65cd94adeccca998b0b6"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,406f16dbbbf8f98709caafe49ca10e21"
+                    [
+                        "ASSEMBLYSCAN",
+                        "assemblyscan",
+                        "1.0.0"
+                    ]
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d3bda95a4a6f65cd94adeccca998b0b6"
+                    ]
+                ],
+                "versions_assemblyscan": [
+                    [
+                        "ASSEMBLYSCAN",
+                        "assemblyscan",
+                        "1.0.0"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2026-01-15T10:01:03.158484579"
+    },
+    "genome.fasta - json": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.json:md5,bcef4e2bf296339c1ca7c513b483de96"
+                    ]
+                ],
+                "1": [
+                    [
+                        "ASSEMBLYSCAN",
+                        "assemblyscan",
+                        "1.0.0"
+                    ]
                 ],
-                "json": [
+                "report": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.json:md5,9140e3d43f2d676f62e1325ace5dd8bd"
+                        "test.json:md5,bcef4e2bf296339c1ca7c513b483de96"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,406f16dbbbf8f98709caafe49ca10e21"
+                "versions_assemblyscan": [
+                    [
+                        "ASSEMBLYSCAN",
+                        "assemblyscan",
+                        "1.0.0"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2026-01-15T10:59:22.469878465"
+    },
+    "genome.fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "ASSEMBLYSCAN",
+                        "assemblyscan",
+                        "1.0.0"
+                    ]
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_assemblyscan": [
+                    [
+                        "ASSEMBLYSCAN",
+                        "assemblyscan",
+                        "1.0.0"
+                    ]
                 ]
             }
         ],
-        "timestamp": "2023-10-18T15:04:38.644743625"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2026-01-15T10:01:08.630557227"
     }
 }