🔧 update image and bioconda container for VueGen to latest version

modules/nf-core/vuegen/environment.yml

@@ -4,5 +4,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - bioconda::vuegen=0.3.2
-  - python=3.11
+  - python=3.12
+  - vuegen=0.5.1

modules/nf-core/vuegen/main.nf

@@ -1,7 +1,9 @@
 process VUEGEN {
     label 'process_single'
     conda "${moduleDir}/environment.yml"
-    container "dtu_biosustain_dsp/vuegen:v0.3.2-nextflow"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fa/fadd4c6459b24fc3964d47d72dbf809e425054e08f1aec9d56c8bec40b4b3a47/data'
+    : 'community.wave.seqera.io/library/vuegen_python:236414fc5cfce774'}"
 
     input:
         val input_type
@@ -18,6 +20,19 @@ process VUEGEN {
     script:
         def args = task.ext.args ?: ''
         """
+        # Set environment variables needed for Quarto rendering
+        # (needed for apptainer/singularity)
+        export XDG_CACHE_HOME="./.xdg_cache_home"
+        export XDG_DATA_HOME="./.xdg_data_home"
+        # Fix Quarto for apptainer: activate conda environment
+        # https://github.com/mahesh-panchal/quarto-docker-singularity-problem
+        ENV_QUARTO="\${ENV_QUARTO:-/opt/conda/etc/conda/activate.d/quarto.sh}"
+        set +u
+        if [ -z "\${QUARTO_DENO}" ] && [ -f "\${ENV_QUARTO}" ]; then
+            source "\${ENV_QUARTO}"
+        fi
+        set -u
+
         # Validate quarto_check flag if using a conda environment
         if [[ "${task.conda}" != "null" ]]; then
             QUARTO_CHECK_FLAG="--quarto_checks"
@@ -36,7 +51,7 @@ process VUEGEN {
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            vuegen: \$( vuegen --version | sed -e "s/vuegen //g" )
+            vuegen: \$( python -c "import vuegen; print(vuegen.__version__)" )
         END_VERSIONS
         """
 
@@ -48,7 +63,7 @@ process VUEGEN {
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            vuegen: \$( vuegen --version | sed -e "s/vuegen //g" )
+            vuegen: \$( python -c "import vuegen; print(vuegen.__version__)" )
         END_VERSIONS
         """
 }

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

@@ -49,7 +49,7 @@ nextflow_process {
                             "Static_Plots.py": path(process.out.output_folder[0] + "/sections/Plots/Static_Plots.py")
                                                 .readLines()[0..3].sort().join('\n').md5()
                         ],
-                        versions: process.out.versions
+                        versions: path(process.out.versions[0]).yaml,
                     ]).match()
                 }
             )
@@ -80,7 +80,7 @@ nextflow_process {
                             "quarto_report.qmd": path(process.out.output_folder[0] + "/quarto_report.qmd")
                                                 .readLines()[0..3].join('\n').md5()
                         ],
-                        versions: process.out.versions
+                        versions: path(process.out.versions[0]).yaml
                     ]).match()
                 }
             )
@@ -111,7 +111,7 @@ nextflow_process {
                             "quarto_report.qmd": path(process.out.output_folder[0] + "/quarto_report.qmd")
                                                     .readLines()[0..3].sort().join('\n').md5()
                         ],
-                        versions: process.out.versions
+                        versions: path(process.out.versions[0]).yaml,
                     ]).match()
                 }
             )
@@ -138,10 +138,10 @@ nextflow_process {
                     assert snapshot(
                         process.out.output_folder.collect { file(it).getName() } +
                         process.out.output_files.collect { file(it).getName() },
-                        versions: process.out.versions
+                        versions: path(process.out.versions[0]).yaml,
                     ).match()
                 }
             )
         }
     }
-}
+}

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

@@ -2,19 +2,21 @@
     "vuegen - directory (HTML report) -stub": {
         "content": [
             {
-                "versions": [
-                    "versions.yml:md5,c3e7ebc433dcacf3d15e1113fd44f5ec"
-                ]
+                "versions": {
+                    "VUEGEN": {
+                        "vuegen": "0.5.1"
+                    }
+                }
             },
             [
                 "report"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "24.10.6"
         },
-        "timestamp": "2025-04-22T09:34:45.900956"
+        "timestamp": "2025-10-20T13:25:42.669804"
     },
     "vuegen - directory (HTML report)": {
         "content": [
@@ -24,16 +26,18 @@
                     "quarto_report.html": "0129d189059f27b3d2ff6f328cd18ef9",
                     "quarto_report.qmd": "e60a379de892055748e4597f9d8c656c"
                 },
-                "versions": [
-                    "versions.yml:md5,c3e7ebc433dcacf3d15e1113fd44f5ec"
-                ]
+                "versions": {
+                    "VUEGEN": {
+                        "vuegen": "0.5.1"
+                    }
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "24.10.6"
         },
-        "timestamp": "2025-04-22T09:04:23.56469"
+        "timestamp": "2025-10-20T13:24:59.558083"
     },
     "vuegen - directory (PDF report)": {
         "content": [
@@ -43,37 +47,41 @@
                     "quarto_report.pdf": true,
                     "quarto_report.qmd": "c447088ca2a435acf926ec5e95c51265"
                 },
-                "versions": [
-                    "versions.yml:md5,c3e7ebc433dcacf3d15e1113fd44f5ec"
-                ]
+                "versions": {
+                    "VUEGEN": {
+                        "vuegen": "0.5.1"
+                    }
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "24.10.6"
         },
-        "timestamp": "2025-04-22T09:05:54.139709"
+        "timestamp": "2025-10-20T13:25:37.140787"
     },
     "vuegen - directory (Streamlit report)": {
         "content": [
             {
                 "output_folder": true,
                 "output_files": {
-                    "Homepage.py": "Homepage.py:md5,483a41696c225663772d68ff2d664493",
-                    "report_manager.py": "report_manager.py:md5,ed15eefa722b7a2f08cca016c0c8e28d",
-                    "All_Formats.py": "e2a56e761eb537da8f9809cbc0b63a9d",
-                    "Interactive_Plots.py": "3198216240ef9b86d5b1ed722bd9b31c",
-                    "Static_Plots.py": "931fd04e2e49cb14d169747b6d5bbd1e"
+                    "Homepage.py": "Homepage.py:md5,a46395bbdfb127463d51d8f601f2ad83",
+                    "report_manager.py": "report_manager.py:md5,a683071ba8bc6e371c8617ef9c3fb84e",
+                    "All_Formats.py": "1f61acc3ca34f6ff941c109d93570815",
+                    "Interactive_Plots.py": "4857dc511178812e93c2037c8bbe04f4",
+                    "Static_Plots.py": "ae9c2e46ae9a9e0e5e98fcce87cd7f80"
                 },
-                "versions": [
-                    "versions.yml:md5,c3e7ebc433dcacf3d15e1113fd44f5ec"
-                ]
+                "versions": {
+                    "VUEGEN": {
+                        "vuegen": "0.5.1"
+                    }
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "24.10.6"
         },
-        "timestamp": "2025-04-22T09:03:48.375488"
+        "timestamp": "2025-10-20T13:19:47.56244"
     }
 }