[module knotAnnotSV] FIX: Merge mutually exclusive outputs into 1 (#11432)

FIX: Mutually exclusive outputs -> merge into 1

Co-authored-by: felix.vandermeeren@chu-montpellier.fr <felix@zazienew.bio2m.local>

Author: tetedange13

modules/nf-core/knotannotsv/main.nf

@@ -11,8 +11,7 @@ process KNOTANNOTSV {
     tuple val(meta), path(annotsv_tsv), val(knot_out_xl)
 
     output:
-    tuple val(meta), path("*.html"), emit: html, optional: true
-    tuple val(meta), path("*.xlsm"), emit: xl, optional: true
+    tuple val(meta), path("*.{html,xlsm}"), emit: output_file
     // CHANGE bellow when UPDATE
     tuple val("${task.process}"), val('knotannotsv'), val('1.1.5'), emit: versions_knotannotsv, topic: versions
 

modules/nf-core/knotannotsv/meta.yml

@@ -1,3 +1,4 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "knotannotsv"
 description: Simple tool to create a customizable html file (to be displayed on
   a web browser) from an AnnotSV output
@@ -32,29 +33,18 @@ input:
         type: boolean
         description: Specify 'true' to output as XLSM (rather than HTML by default)
 output:
-  html:
+  output_file:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
-      - "*.html":
+      - "*.{html,xlsm}":
           type: file
-          description: HTML annotated file
-          pattern: "*.html"
+          description: HTML (or XLSM if 'knot_out_xl=true') annotated file
+          pattern: "*.{html,xlsm}"
           ontologies:
             - edam: "http://edamontology.org/format_2331" # HTML
-  xl:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'sample1' ]`
-      - "*.xlsm":
-          type: file
-          description: Alternative XLSM annotated file (if 'knot_out_xl=true')
-          pattern: "*.xlsm"
-          ontologies:
             - edam: "http://edamontology.org/format_3620" # XLSX
   versions_knotannotsv:
     - - ${task.process}:

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

@@ -33,7 +33,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.findAll { key, val -> key.startsWith('versions') },
-                    "test_HTML_output_lines_count: ${path(process.out.html[0][1]).readLines().size()}"
+                    "test_HTML_output_lines_count: ${path(process.out.output_file[0][1]).readLines().size()}"
                     ).match()
                 }
             )
@@ -63,7 +63,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.findAll { key, val -> key.startsWith('versions') },
-                    "test_Excel_output_min_size: ${file(process.out.xl[0][1]).length() >= 89000}"
+                    "test_Excel_output_min_size: ${file(process.out.output_file[0][1]).length() >= 89000}"
                     ).match()
                 }
             )

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

@@ -2,30 +2,27 @@
     "homo_sapiens - annotsv_tsv, knot_out_xl - stub - XLSM output": {
         "content": [
             {
-                "html": [
-                    
+                "output_file": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.xlsm:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "versions_knotannotsv": [
                     [
                         "KNOTANNOTSV",
                         "knotannotsv",
                         "1.1.5"
                     ]
-                ],
-                "xl": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.xlsm:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
                 ]
             }
         ],
-        "timestamp": "2026-04-09T10:42:35.523232226",
+        "timestamp": "2026-04-30T11:58:24.702285389",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "26.03.0"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.2"
         }
     },
     "homo_sapiens - annotsv_tsv, knot_out_xl - XLSM output": {
@@ -41,10 +38,10 @@
             },
             "test_Excel_output_min_size: true"
         ],
-        "timestamp": "2026-04-08T16:46:37.607548934",
+        "timestamp": "2026-04-30T11:58:04.22923394",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "26.03.0"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.2"
         }
     },
     "homo_sapiens - annotsv_tsv, knot_out_xl - HTML output": {
@@ -60,16 +57,16 @@
             },
             "test_HTML_output_lines_count: 5249"
         ],
-        "timestamp": "2026-04-08T16:46:25.466379551",
+        "timestamp": "2026-04-30T11:57:52.944222502",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "26.03.0"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.2"
         }
     },
     "homo_sapiens - annotsv_tsv, knot_out_xl - stub - HTML output": {
         "content": [
             {
-                "html": [
+                "output_file": [
                     [
                         {
                             "id": "test"
@@ -83,16 +80,13 @@
                         "knotannotsv",
                         "1.1.5"
                     ]
-                ],
-                "xl": [
-                    
                 ]
             }
         ],
-        "timestamp": "2026-04-09T10:42:24.714283695",
+        "timestamp": "2026-04-30T11:58:14.502123897",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "26.03.0"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.2"
         }
     }
 }

modules/nf-core/knotannotsv/tests/nextflow.config

@@ -1,5 +1,5 @@
 process {
     withName: KNOTANNOTSV {
-        ext.args   = params.module_args
+        ext.args = params.module_args
     }
 }