Update to topic qcat

modules/nf-core/qcat/main.nf

@@ -9,11 +9,11 @@ process QCAT {
 
     input:
     tuple val(meta), path(reads)
-    val   barcode_kit
+    val barcode_kit
 
     output:
     tuple val(meta), path("fastq/*.fastq.gz"), emit: reads
-    path "versions.yml"                      , emit: versions
+    tuple val("${task.process}"), val('qcat'), eval("qcat --version | sed 's/.*qcat //;s/ .*//'"), emit: versions_qcat, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,39 +22,27 @@ process QCAT {
     """
     ## Unzip fastq file
     ## qcat doesn't support zipped files yet
-    FILE=$reads
+    FILE=${reads}
     if [[ \$FILE == *.gz ]]
     then
-        zcat $reads > unzipped.fastq
+        zcat ${reads} > unzipped.fastq
         FILE=unzipped.fastq
     fi
 
     qcat \\
         -f \$FILE \\
         -b ./fastq \\
-        --kit $barcode_kit
+        --kit ${barcode_kit}
 
     ## Zip fastq files
     gzip fastq/*
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        qcat: \$(qcat --version | sed 's/^.*qcat //; s/ .*\$//')
-    END_VERSIONS
     """
 
     stub:
     """
     mkdir -p fastq
 
-    touch fastq/barcode00.fastq
-    touch fastq/none.fastq
-
-    gzip fastq/*
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        qcat: \$(qcat --version | sed 's/^.*qcat //; s/ .*\$//')
-    END_VERSIONS
+    echo "" | gzip > fastq/barcode00.fastq.gz
+    echo "" | gzip > fastq/none.fastq.gz
     """
 }

modules/nf-core/qcat/meta.yml

@@ -10,7 +10,8 @@ tools:
         A demultiplexer for Nanopore samples
       homepage: https://github.com/nanoporetech/qcat
       documentation: https://github.com/nanoporetech/qcat#qcat
-      licence: ["MPL-2.0"]
+      licence:
+        - "MPL-2.0"
       identifier: ""
 input:
   - - meta:
@@ -39,13 +40,29 @@ output:
           pattern: "*.fastq.gz"
           ontologies:
             - edam: http://edamontology.org/format_3989 # GZIP format
+  versions_qcat:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - qcat:
+          type: string
+          description: The name of the tool
+      - qcat --version | sed 's/.*qcat //;s/ .*//':
+          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
+      - qcat:
+          type: string
+          description: The name of the tool
+      - qcat --version | sed 's/.*qcat //;s/ .*//':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@yuukiiwa"
   - "@drpatelh"

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

@@ -15,7 +15,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test' ], // meta map
+                    [ id:'test' ],
 				    [ file("https://github.com/nf-core/test-datasets/raw/nanoseq/fastq/nondemultiplexed/sample_nobc_dx.fastq.gz", checkIfExists: true) ]
 				]
 				input[1] = 'NBD103/NBD104'
@@ -27,38 +27,30 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.reads,
-                    process.out.versions,
-                    file(process.out.versions[0]).readLines()[1].trim() // trap to catch conda version mismatches
-                    ).match()
-                }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
 
     test("test-qcat-stub") {
         options '-stub'
-
         when {
             process {
                 """
                 input[0] = [
-                    [ id:'test' ], // meta map
+                    [ id:'test' ],
 				    [ file("https://github.com/nf-core/test-datasets/raw/nanoseq/fastq/nondemultiplexed/sample_nobc_dx.fastq.gz", checkIfExists: true) ]
 				]
 				input[1] = 'NBD103/NBD104'
-
                 """
             }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
-
 }

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

@@ -1,66 +1,61 @@
 {
     "test-qcat": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
+            {
+                "reads": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "barcode06.fastq.gz:md5,f02509a0edada5bde143a2155969eaaa",
+                            "barcode12.fastq.gz:md5,e3dda1db83ad2895ff95b3612b9f4348",
+                            "none.fastq.gz:md5,36ed3f5964a59532b75a7f0c5975ecc6"
+                        ]
+                    ]
+                ],
+                "versions_qcat": [
                     [
-                        "barcode06.fastq.gz:md5,f02509a0edada5bde143a2155969eaaa",
-                        "barcode12.fastq.gz:md5,e3dda1db83ad2895ff95b3612b9f4348",
-                        "none.fastq.gz:md5,36ed3f5964a59532b75a7f0c5975ecc6"
+                        "QCAT",
+                        "qcat",
+                        "1.1.0"
                     ]
                 ]
-            ],
-            [
-                "versions.yml:md5,78ca985d3d7741b521d87af6eb190f30"
-            ],
-            "qcat: 1.1.0"
+            }
         ],
+        "timestamp": "2026-08-07T15:28:18.380966741",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-29T12:36:04.213621"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     },
     "test-qcat-stub": {
         "content": [
             {
-                "0": [
+                "reads": [
                     [
                         {
                             "id": "test"
                         },
                         [
-                            "barcode00.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "none.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            "barcode00.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "none.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                         ]
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,78ca985d3d7741b521d87af6eb190f30"
-                ],
-                "reads": [
+                "versions_qcat": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "barcode00.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "none.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
+                        "QCAT",
+                        "qcat",
+                        "1.1.0"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,78ca985d3d7741b521d87af6eb190f30"
                 ]
             }
         ],
+        "timestamp": "2026-08-07T15:28:28.814302286",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-29T12:34:55.736959"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }