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

@@ -4,23 +4,28 @@ 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("*.tsv"),     emit: tsv, optional: true
+    tuple val(meta), path("*.json"),    emit: json, optional: true
+    path "versions.yml",                emit: versions
 
     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 ${assembly} > ${prefix}.json
+    assembly-scan \\
+         ${args} \\
+         ${assembly} > ${prefix}.${file_format}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/assemblyscan/meta.yml

@@ -25,6 +25,18 @@ input:
         pattern: "*.fasta"
         ontologies: []
 output:
+  tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tsv":
+          type: file
+          description: Assembly statistics in tsv format
+          pattern: "*.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
   json:
     - - meta:
           type: map
@@ -47,6 +59,8 @@ output:
 authors:
   - "@sateeshperi"
   - "@mjcipriano"
+  - "@eit-maxlcummins"
 maintainers:
   - "@sateeshperi"
   - "@mjcipriano"
+  - "@eit-maxlcummins"

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

@@ -8,26 +8,36 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.json:md5,9140e3d43f2d676f62e1325ace5dd8bd"
+                        "test.tsv:md5,d3bda95a4a6f65cd94adeccca998b0b6"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,406f16dbbbf8f98709caafe49ca10e21"
+
+                ],
+                "2": [
+                    "versions.yml:md5,4113de9fcbbd8f6fc66a5abc7720aa62"
                 ],
                 "json": [
+
+                ],
+                "tsv": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.json:md5,9140e3d43f2d676f62e1325ace5dd8bd"
+                        "test.tsv:md5,d3bda95a4a6f65cd94adeccca998b0b6"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,406f16dbbbf8f98709caafe49ca10e21"
+                    "versions.yml:md5,4113de9fcbbd8f6fc66a5abc7720aa62"
                 ]
             }
         ],
-        "timestamp": "2023-10-18T15:04:38.644743625"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-12-04T16:48:44.200207939"
     }
 }

modules/nf-core/trinity/main.nf

@@ -70,4 +70,4 @@ process TRINITY {
     gzip ${prefix}.fa
     touch ${prefix}.log
     """
-}
+}

modules/nf-core/trinity/meta.yml

@@ -77,4 +77,4 @@ authors:
   - "@gallvp"
 maintainers:
   - "@timslittle"
-  - "@gallvp"
+  - "@gallvp"