Adjust deacon/index based on PR feedback

Author: mberacochea

modules/nf-core/deacon/index/main.nf

@@ -19,7 +19,7 @@ process DEACON_INDEX {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${fasta.baseName}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     deacon \\
         index \\

modules/nf-core/deacon/index/meta.yml

@@ -8,6 +8,7 @@ keywords:
   - genome
   - reference
   - minimizer
+  - decontamination
 tools:
   - "deacon":
       description: "Fast alignment-free sequence filter"
@@ -27,7 +28,7 @@ input:
     - fasta:
         type: file
         description: Input genome fasta file
-        pattern: "*.{fasta,fa,fas,fna}"
+        pattern: "*.{fasta,fasta.gz,fas,fas.gz,fa,fa.gz,fna,fna.gz}"
         ontologies:
           - edam: "http://edamontology.org/data_2044" # Sequence
           - edam: "http://edamontology.org/format_1929" # FASTA

modules/nf-core/deacon/index/tests/main.nf.test

@@ -25,7 +25,36 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                        process.out.index,
+                        process.out.versions.collect { path(it).yaml }
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("index sarscov2 - fasta gzipped") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    process.out.versions.collect{ path(it).yaml }
+                ).match() }
             )
         }
 
@@ -49,10 +78,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    process.out.versions.collect{ path(it).yaml }
+                ).match() }
             )
         }
-
     }
-
 }

modules/nf-core/deacon/index/tests/main.nf.test.snap

@@ -1,13 +1,37 @@
 {
     "index sarscov2 - fasta": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.idx:md5,7437b25e6659ebfd5cf9be7b325f90c3"
+                ]
+            ],
+            [
+                {
+                    "DEACON_INDEX": {
+                        "deacon": "0.5.0"
+                    }
+                }
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.3"
+        },
+        "timestamp": "2025-06-16T08:54:38.622063"
+    },
+    "index sarscov2 - fasta - stub": {
         "content": [
             {
                 "0": [
                     [
                         {
                             "id": "test"
                         },
-                        "genome.idx:md5,7437b25e6659ebfd5cf9be7b325f90c3"
+                        "genome.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -18,29 +42,36 @@
                         {
                             "id": "test"
                         },
-                        "genome.idx:md5,7437b25e6659ebfd5cf9be7b325f90c3"
+                        "genome.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,60749febc4eaab16229dc078af00ea27"
                 ]
-            }
+            },
+            [
+                {
+                    "DEACON_INDEX": {
+                        "deacon": "0.5.0"
+                    }
+                }
+            ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.3"
         },
-        "timestamp": "2025-06-15T23:31:07.423054"
+        "timestamp": "2025-06-16T12:31:10.825365"
     },
-    "index sarscov2 - fasta - stub": {
+    "index sarscov2 - fasta gzipped": {
         "content": [
             {
                 "0": [
                     [
                         {
                             "id": "test"
                         },
-                        "genome.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.idx:md5,7437b25e6659ebfd5cf9be7b325f90c3"
                     ]
                 ],
                 "1": [
@@ -51,18 +82,25 @@
                         {
                             "id": "test"
                         },
-                        "genome.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.idx:md5,7437b25e6659ebfd5cf9be7b325f90c3"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,60749febc4eaab16229dc078af00ea27"
                 ]
-            }
+            },
+            [
+                {
+                    "DEACON_INDEX": {
+                        "deacon": "0.5.0"
+                    }
+                }
+            ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.3"
         },
-        "timestamp": "2025-06-15T23:31:10.744238"
+        "timestamp": "2025-06-16T12:31:07.212408"
     }
 }