🔧 update image and bioconda container for VueGen to latest version

modules/nf-core/vuegen/Dockerfile

@@ -0,0 +1,52 @@
+# Set the base image to the official Python 3.12 slim debian trixie image
+FROM python:3.12-slim-trixie
+
+
+# Disable manual feedback for apt-get, update package list, install security updates,
+# and install packages (procps, and system dependencies for tinytex and kaleido).
+# Then clean up the package list and remove the cache.
+RUN export DEBIAN_FRONTEND=noninteractive && \
+    apt-get update && \
+    apt-get -y upgrade && \
+    apt-get install -y --no-install-recommends \
+    procps=2:4.0.4-9 \
+    wget=1.25.0-2 \
+    perl=5.40.1-6 \
+    # #2.84.4-3~deb13u1
+    libglib2.0-0t64=2.84.4-3~deb13u1 \
+    libgdk-pixbuf-2.0-0=2.42.12+dfsg-4 \
+    libfontconfig1=2.15.0-2.3 \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install vuegen Python package
+RUN pip install --no-cache-dir -U vuegen==0.5.1
+
+# Create and switch to non-root user for security reasons
+RUN useradd --create-home appuser
+USER appuser
+
+# Set the working directory
+WORKDIR /home/appuser
+
+# Install TinyTeX for pdf reports
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+RUN perl -mFile::Find /dev/null && \
+    wget -qO- "https://yihui.org/tinytex/install-bin-unix.sh" | sh && \
+    ~/.TinyTeX/bin/*/tlmgr \
+    install \
+    koma-script \
+    caption \
+    luaotfload
+
+# Set permissions for the appuser home directory
+RUN chmod -R 777 /home/appuser
+
+# Set environment variables for Quarto, dataframe_image, and TinyTeX. Also, get tracebacks from C crashes
+ENV XDG_RUNTIME_DIR=/tmp \
+    XDG_CACHE_HOME=/tmp/quarto_cache_home \
+    XDG_DATA_HOME=/tmp/quarto_data_home \
+    PATH="${PATH}:/home/appuser/bin" \
+    TEXMFVAR=/tmp/texmf-var \
+    TEXMFHOME=/tmp/texmf-home \
+    PYTHONFAULTHANDLER=1

modules/nf-core/vuegen/README.md

@@ -0,0 +1,22 @@
+# VueGen Module
+
+## Dockerimage
+
+The dockerimage is needed as both quarto and the TinyTeX distribution are installed
+inside the container to make vuegen work properly. At runtime especially apptainer
+does not support installing packages on the fly to read-only directories.
+
+```bash
+#!/bin/bash
+set -euo pipefail
+
+ORG="quay.io/nf-core"
+VERSION="v0.5.1"
+
+# 1. Build & push the base image (nextflow version)
+docker buildx build \
+  --platform linux/amd64,linux/arm64 \
+  --push \
+  -t ${ORG}/vuegen:${VERSION} \
+  -f Dockerfile .
+```

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

@@ -1,23 +1,23 @@
 process VUEGEN {
     label 'process_single'
     conda "${moduleDir}/environment.yml"
-    container "dtu_biosustain_dsp/vuegen:v0.3.2-nextflow"
+    container "nf-core/vuegen:0.5.1"
 
     input:
-        val input_type
-        path input_path
-        val report_type
+    val input_type
+    path input_path
+    val report_type
 
     output:
-        path "*report", emit: output_folder
-        path "versions.yml", emit: versions
+    path "*report", emit: output_folder
+    path "versions.yml", emit: versions
 
     when:
-        task.ext.when == null || task.ext.when
+    task.ext.when == null || task.ext.when
 
     script:
-        def args = task.ext.args ?: ''
-        """
+    def args = task.ext.args ?: ''
+    """
         # Validate quarto_check flag if using a conda environment
         if [[ "${task.conda}" != "null" ]]; then
             QUARTO_CHECK_FLAG="--quarto_checks"
@@ -27,28 +27,28 @@ process VUEGEN {
 
         # Execute VueGen based on the input type
         if [ "${input_type}" == "config" ]; then
-            echo "Running VueGen with config file: $input_path"
-            vuegen --config $input_path --report_type $report_type \$QUARTO_CHECK_FLAG $args
+            echo "Running VueGen with config file: ${input_path}"
+            vuegen --config ${input_path} --report_type ${report_type} \$QUARTO_CHECK_FLAG ${args}
         elif [ "${input_type}" == "directory" ]; then
-            echo "Running VueGen with directory: $input_path"
-            vuegen --directory $input_path --report_type $report_type \$QUARTO_CHECK_FLAG $args
+            echo "Running VueGen with directory: ${input_path}"
+            vuegen --directory ${input_path} --report_type ${report_type} \$QUARTO_CHECK_FLAG ${args}
         fi
 
         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
         """
 
     stub:
-        """
+    """
         echo "STUB MODE: Creating a generic report directory"
         mkdir -p report
         touch report/report.txt
 
         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()
                 }
             )
@@ -138,7 +138,7 @@ 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"
     }
 }