update CADD version to 1.7.3

modules/nf-core/cadd/environment.yml

@@ -4,6 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::cadd-scripts=1.6.post1
-  - conda-forge::conda=4.14.0
-  - conda-forge::mamba=1.4.0
+  - bioconda::cadd-scripts=1.7.3

modules/nf-core/cadd/main.nf

@@ -3,24 +3,28 @@ process CADD {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container 'docker.io/biocontainers/cadd-scripts-with-envs:1.6.post1_cv1'
-
-    containerOptions "${ prescored_dir ?
-        ['singularity', 'apptainer'].contains(workflow.containerEngine) ?
-            "-B ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations -B ${prescored_dir}:/opt/CADD-scripts-1.6.post1/data/prescored" :
-            "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations -v ${prescored_dir}:/opt/CADD-scripts-1.6.post1/data/prescored" :
-        ['singularity', 'apptainer'].contains(workflow.containerEngine) ?
-            "-B ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" :
-            "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" }"
+    container 'docker.io/clinicalgenomics/cadd-with-scripts:1.7.3'
+
+    containerOptions {
+        if (prescored_dir) {
+            ['singularity', 'apptainer'].contains(workflow.containerEngine) ?
+                "-B ${annotation_dir}:/cadd-scripts/data/annotations -B ${prescored_dir}:/cadd-scripts/data/prescored" :
+                "-v ${annotation_dir}:/cadd-scripts/data/annotations -v ${prescored_dir}:/cadd-scripts/data/prescored"
+        } else {
+            ['singularity', 'apptainer'].contains(workflow.containerEngine) ?
+                "-B ${annotation_dir}:/cadd-scripts/data/annotations" :
+                "-v ${annotation_dir}:/cadd-scripts/data/annotations"
+        }
+    }
 
     input:
     tuple val(meta), path(vcf)
-    tuple val(meta2), path(annotation_dir)
-    tuple val(meta3), path(prescored_dir)
+    tuple val(meta2), val(annotation_dir)
+    tuple val(meta3), val(prescored_dir)
 
     output:
     tuple val(meta), path("${prefix}.tsv.gz"), emit: tsv
-    tuple val("${task.process}"), val("cadd"), val("1.6.post1"), emit: versions_cadd, topic: versions
+    tuple val("${task.process}"), val("cadd"), val("1.7.3"), emit: versions_cadd, topic: versions
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
 
     when:
@@ -31,9 +35,11 @@ process CADD {
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     export XDG_CACHE_HOME=\$PWD/snakemake_cache
+    export MPLCONFIGDIR=.
     mkdir -p \$XDG_CACHE_HOME
 
-    cadd.sh \\
+    CADD.sh \\
+        -m \\
         -o ${prefix}.tsv.gz \\
         ${args} \\
         ${vcf}

modules/nf-core/cadd/meta.yml

@@ -44,8 +44,16 @@ input:
     - prescored_dir:
         type: directory
         description: |
-          Path to folder containing prescored files.
-          This folder contains the uncompressed files that would otherwise be in data/prescored/${GENOME_BUILD}_${VERSION}/ folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.
+          Path to folder containing prescored CADD score files.
+          Expected structure mirrors data/prescored/ from the CADD-scripts installation:
+            <prescored_dir>/
+              GRCh38_v1.7/
+                incl_anno/   # *.tsv.gz + *.tsv.gz.tbi (scores with annotations)
+                no_anno/     # *.tsv.gz + *.tsv.gz.tbi (scores only)
+              GRCh37_v1.7/
+                incl_anno/
+                no_anno/
+          See https://github.com/kircherlab/CADD-scripts/#manual-installation for details.
 output:
   tsv:
     - - meta:
@@ -66,7 +74,7 @@ output:
       - cadd:
           type: string
           description: The name of the tool
-      - 1.6.post1:
+      - 1.7.3:
           type: string
           description: The expression to obtain the version of the tool
 topics:
@@ -77,7 +85,7 @@ topics:
       - cadd:
           type: string
           description: The name of the tool
-      - 1.6.post1:
+      - 1.7.3:
           type: string
           description: The expression to obtain the version of the tool
 authors:

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

@@ -9,6 +9,8 @@ nextflow_process {
     tag "modules_nfcore"
     tag "cadd"
 
+    config "./nextflow.config"
+
     test("test_cadd - stub") {
         options '-stub'
         when {

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

@@ -15,7 +15,7 @@
                     [
                         "CADD",
                         "cadd",
-                        "1.6.post1"
+                        "1.7.3"
                     ]
                 ],
                 "tsv": [
@@ -31,15 +31,15 @@
                     [
                         "CADD",
                         "cadd",
-                        "1.6.post1"
+                        "1.7.3"
                     ]
                 ]
             },
             [
 
             ]
         ],
-        "timestamp": "2026-02-19T20:06:20.885977",
+        "timestamp": "2026-03-01T12:08:37.372500636",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"

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

@@ -0,0 +1,5 @@
+process {
+    withName: 'CADD' {
+        container = "nf-core/ubuntu:22.04" //Using an basic container because v1.7.3 is too big for CI.
+    }
+}