Fix flag logic in caddsv-get

modules/nf-core/caddsv/get/main.nf

@@ -1,12 +1,16 @@
 process CADDSV_GET {
-    tag 'CADDSV annotations'
+    tag "CADDSV ${flag}"
     label 'process_single'
+    label 'process_long'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/caddsv:2.0--pyh84cbfca_0':
         'quay.io/biocontainers/caddsv:2.0--pyh84cbfca_0' }"
 
+    input:
+    val flag
+
     output:
     path "caddsv_annotations", emit: annotations
     tuple val("${task.process}"), val('caddsv'), eval("python -c \"import importlib.metadata as m; print(m.version('caddsv'))\""), emit: versions_caddsv, topic: versions
@@ -16,17 +20,23 @@ process CADDSV_GET {
 
     script:
     def args = task.ext.args ?: ''
+
+    if (!['annotations', 'segmentnt'].contains(flag)) {
+        error "Invalid caddsv get flag: '${flag}'. Expected 'annotations' or 'segmentnt'."
+    }
+
     """
-    caddsv get \\
+    set -euo pipefail
+
+    caddsv get ${flag} \\
         --annotations-dir "caddsv_annotations" \\
         ${args}
+
+    test -d caddsv_annotations
     """
 
     stub:
-    def args = task.ext.args ?: ''
     """
-    echo $args
-
     mkdir -p caddsv_annotations
     touch caddsv_annotations/stub.txt
     """

modules/nf-core/caddsv/get/meta.yml

@@ -1,11 +1,13 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "caddsv_get"
-description: Download CADD-SV annotation resources and, optionally, SegmentNT model files.
+description: Download CADD-SV annotation resources or SegmentNT model files.
 keywords:
   - caddsv
   - structural variants
   - annotations
+  - segmentnt
   - resource download
+
 tools:
   - "caddsv":
       description: "CADD-SV is a command-line tool for scoring structural variants (SVs)"
@@ -17,16 +19,26 @@ tools:
         - "MIT"
       identifier: "biotools:cadd-sv"
 
-input: []
+input:
+  - flag:
+      type: string
+      description: >
+        CADD-SV resource flag to download. Use `annotations` to download the
+        CADD-SV annotation bundle, or `segmentnt` to download only the SegmentNT
+        model files into `<annotations-dir>/segment_nt`.
+      pattern: "annotations|segmentnt"
+      ontologies: []
 
 output:
   annotations:
     - caddsv_annotations:
         type: directory
         description: >
-          Directory containing downloaded CADD-SV annotations. If `--with-segmentnt`
-          is supplied via `task.ext.args`, this directory will also contain the SegmentNT model
-          files under `segment_nt/`.
+          Directory containing downloaded CADD-SV resources. If `flag` is
+          `annotations`, this contains the CADD-SV annotation bundle. If
+          `flag` is `segmentnt`, this contains SegmentNT files under
+          `segment_nt/`. If `flag` is `annotations` and `--with-segmentnt`
+          is supplied via `task.ext.args`, this contains both resources.
         pattern: "caddsv_annotations"
         ontologies: []
 
@@ -55,5 +67,6 @@ topics:
 
 authors:
   - "@manascripts"
+
 maintainers:
   - "@manascripts"

modules/nf-core/caddsv/get/tests/main.nf.test

@@ -9,17 +9,43 @@ nextflow_process {
     tag "caddsv"
     tag "caddsv/get"
 
-    test("caddsv-get - stub") {
+    test("caddsv-get annotations - stub") {
 
         options "-stub"
 
+        when {
+            process {
+                """
+                input[0] = Channel.value('annotations')
+                """
+            }
+        }
+
         then {
             assert process.success
             assertAll(
                 { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
 
+    test("caddsv-get segmentnt - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.value('segmentnt')
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
 }

modules/nf-core/caddsv/get/tests/main.nf.test.snap

@@ -1,5 +1,5 @@
 {
-    "caddsv-get - stub": {
+    "caddsv-get annotations - stub": {
         "content": [
             {
                 "annotations": [
@@ -16,7 +16,30 @@
                 ]
             }
         ],
-        "timestamp": "2026-06-10T13:47:54.858373568",
+        "timestamp": "2026-06-23T16:33:17.869563355",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "caddsv-get segmentnt - stub": {
+        "content": [
+            {
+                "annotations": [
+                    [
+                        "stub.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_caddsv": [
+                    [
+                        "CADDSV_GET",
+                        "caddsv",
+                        "2.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-06-23T16:33:23.758487333",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"