lint + code polish controlfreec

.github/workflows/nf-test-gpu.yml

@@ -30,7 +30,7 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
-  NXF_VER: "24.10.2"
+  NXF_VER: "25.04.6"
 
 jobs:
   nf-test-changes:

.github/workflows/nf-test.yml

@@ -28,7 +28,7 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
-  NXF_VER: "24.10.2"
+  NXF_VER: "25.04.6"
 
 jobs:
   nf-test-changes:

.github/workflows/pytest-workflow.yml

@@ -108,8 +108,6 @@ jobs:
             tags: checkm2/databasedownload
           - profile: conda
             tags: checkm2/predict
-          - profile: conda
-            tags: controlfreec/makegraph2
           - profile: conda
             tags: deepcell/mesmer
           - profile: conda

.github/workflows/update-gpu-snapshot.yml

@@ -10,7 +10,7 @@ env:
   NFT_VER: "0.9.2"
   NXF_ANSI_LOG: false
   # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
-  NXF_VER: "24.10.2"
+  NXF_VER: "25.04.6"
 
 jobs:
   update-gpu-snapshot:

.github/workflows/update-sentieon-snapshot.yml

@@ -10,7 +10,7 @@ env:
   NFT_VER: "0.9.2"
   NXF_ANSI_LOG: false
   # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
-  NXF_VER: "24.10.2"
+  NXF_VER: "25.04.6"
 
 jobs:
   update-sentieon-snapshot:

.github/workflows/wave.yml

@@ -15,7 +15,7 @@ env:
   # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
   NFT_VER: "0.9.2"
   # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
-  NXF_VER: "24.10.1"
+  NXF_VER: "25.04.6"
 
 jobs:
   generate-matrix:

modules/nf-core/controlfreec/assesssignificance/main.nf

@@ -1,46 +1,47 @@
 process CONTROLFREEC_ASSESSSIGNIFICANCE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' :
-        'biocontainers/control-freec:11.6b--hdbdd923_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0'
+        : 'biocontainers/control-freec:11.6b--hdbdd923_0'}"
 
     input:
     tuple val(meta), path(cnvs), path(ratio)
 
     output:
     tuple val(meta), path("*.p.value.txt"), emit: p_value_txt
-    path "versions.yml"                   , emit: versions
+    path "versions.yml",                    emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = "11.6b"
     """
     cat \$(which assess_significance.R) | R --slave --args ${cnvs} ${ratio}
 
     mv *.p.value.txt ${prefix}.p.value.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: $VERSION
+        controlfreec: ${VERSION}
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = "11.6b"
     """
     touch ${prefix}.p.value.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: $VERSION
+        controlfreec: ${VERSION}
     END_VERSIONS
     """
 }

modules/nf-core/controlfreec/assesssignificance/tests/main.nf.test.snap

@@ -31,10 +31,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-03-26T16:24:34.84551"
+        "timestamp": "2025-09-08T08:58:22.551535272"
     },
     "version": {
         "content": [
@@ -43,9 +43,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-03-26T17:23:22.833417"
+        "timestamp": "2025-09-08T08:58:06.212126105"
     }
 }