🔧 update image and bioconda container for VueGen to latest version

modules/nf-core/vuegen/Dockerfile

@@ -0,0 +1,45 @@
+# Set the base image to the official Python 3.12 slim debian bookworm image
+FROM python:3.12-slim-bookworm
+
+# 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 \
+    wget \
+    perl \
+    libglib2.0-0 \
+    libgdk-pixbuf2.0-0 \
+    libfontconfig1 \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install vuegen Python package
+RUN pip install --no-cache-dir -U vuegen
+
+# 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
+RUN perl -mFile::Find /dev/null && \
+    wget -qO- "https://yihui.org/tinytex/install-bin-unix.sh" | sh && \
+    ~/.TinyTeX/bin/*/tlmgr install \
+    koma-script \
+    caption
+
+# 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" \
+    PYTHONFAULTHANDLER=1

modules/nf-core/vuegen/README.md

@@ -0,0 +1,27 @@
+# VueGen module
+
+## Images using wave
+
+Cached images for 0.5.1 version available on wave, see 
+[docs](https://docs.seqera.io/wave#seqera-containers---the-community-container-registry)
+
+platform    | version     | image
+--------    | -------     | -----
+docker      | linux/amd64 | community.wave.seqera.io/library/vuegen_python:236414fc5cfce774
+singularity | linux/amd64 | oras://community.wave.seqera.io/library/vuegen_python:1adb57ecbfa02088
+docker      | linux/arm64 | community.wave.seqera.io/library/vuegen_python:a1dc6490f5045706
+singularity | linux/arm64 | oras://community.wave.seqera.io/library/vuegen_python:64670fcadedf151f
+
+## Custom docker file
+
+- check Docker best practices with hadolint, see
+ [docker-docs](https://docs.docker.com/build/building/best-practices/)
+
+
+```bash
+$ hadolint Dockerfile
+Dockerfile:7 DL3008 warning: Pin versions in apt get install. Instead of `apt-get install <package>` use `apt-get install <package>=<version>`
+Dockerfile:24 DL3059 info: Multiple consecutive `RUN` instructions. Consider consolidation.
+Dockerfile:31 SC2211 warning: This is a glob used as a command name. Was it supposed to be in ${..}, array, or is it missing quoting?
+Dockerfile:31 DL4006 warning: Set the SHELL option -o pipefail before RUN with a pipe in it. If you are using /bin/sh in an alpine image or if your shell is symlinked to busybox then consider explicitly setting your SHELL to /bin/ash, or disable this check
+```

modules/nf-core/vuegen/environment.yml

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

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
+    ? 'oras://community.wave.seqera.io/library/vuegen_python:1adb57ecbfa02088'
+    : 'community.wave.seqera.io/library/vuegen_python:236414fc5cfce774'}"
 
     input:
         val input_type
@@ -36,7 +38,7 @@ 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 +50,7 @@ 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"
     }
 }