From fd604a18070cf4cfd2c8956bf7949abeab55f33a Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Thu, 16 Oct 2025 15:01:25 +0200 Subject: [PATCH 01/12] =?UTF-8?q?=F0=9F=94=A7=20update=20image=20and=20bio?= =?UTF-8?q?conda=20container=20to=20latest=20version?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- modules/nf-core/vuegen/environment.yml | 2 +- modules/nf-core/vuegen/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/vuegen/environment.yml b/modules/nf-core/vuegen/environment.yml index 8eab2a170585..b007e4c77c6d 100644 --- a/modules/nf-core/vuegen/environment.yml +++ b/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 diff --git a/modules/nf-core/vuegen/main.nf b/modules/nf-core/vuegen/main.nf index ddc333fe5859..ad2733b2db43 100644 --- a/modules/nf-core/vuegen/main.nf +++ b/modules/nf-core/vuegen/main.nf @@ -1,7 +1,7 @@ process VUEGEN { label 'process_single' conda "${moduleDir}/environment.yml" - container "dtu_biosustain_dsp/vuegen:v0.3.2-nextflow" + container "dtu_biosustain_dsp/vuegen:v0.5.1-nextflow" input: val input_type From a1d39a879d04c30eaf79fedb2d6bafcbeb5df90d Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Thu, 16 Oct 2025 15:35:12 +0200 Subject: [PATCH 02/12] =?UTF-8?q?=E2=9C=85=20update=20test=20snapshots?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- modules/nf-core/vuegen/tests/main.nf.test.snap | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/modules/nf-core/vuegen/tests/main.nf.test.snap b/modules/nf-core/vuegen/tests/main.nf.test.snap index ba5f6682404c..cf75e8f10c71 100644 --- a/modules/nf-core/vuegen/tests/main.nf.test.snap +++ b/modules/nf-core/vuegen/tests/main.nf.test.snap @@ -59,11 +59,11 @@ { "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" @@ -72,8 +72,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "24.10.6" }, - "timestamp": "2025-04-22T09:03:48.375488" + "timestamp": "2025-10-16T15:32:46.503388" } } \ No newline at end of file From 5eb02c415a410536f9897d83fc0a53cf3b2b2848 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Mon, 20 Oct 2025 11:32:12 +0200 Subject: [PATCH 03/12] :bug: fix display of version of vuegen - had no command line interface option to display version, see https://github.com/Multiomics-Analytics-Group/vuegen/issues/167 --- modules/nf-core/vuegen/main.nf | 4 ++-- .../nf-core/vuegen/tests/main.nf.test.snap | 22 +++++++++---------- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/modules/nf-core/vuegen/main.nf b/modules/nf-core/vuegen/main.nf index ad2733b2db43..53e8156a1e6d 100644 --- a/modules/nf-core/vuegen/main.nf +++ b/modules/nf-core/vuegen/main.nf @@ -36,7 +36,7 @@ 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 +48,7 @@ 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 """ } diff --git a/modules/nf-core/vuegen/tests/main.nf.test.snap b/modules/nf-core/vuegen/tests/main.nf.test.snap index cf75e8f10c71..4b31649c8c8f 100644 --- a/modules/nf-core/vuegen/tests/main.nf.test.snap +++ b/modules/nf-core/vuegen/tests/main.nf.test.snap @@ -3,7 +3,7 @@ "content": [ { "versions": [ - "versions.yml:md5,c3e7ebc433dcacf3d15e1113fd44f5ec" + "versions.yml:md5,ab1c484af3dc5362a395914456c42569" ] }, [ @@ -12,9 +12,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "24.10.6" }, - "timestamp": "2025-04-22T09:34:45.900956" + "timestamp": "2025-10-20T11:23:58.208613" }, "vuegen - directory (HTML report)": { "content": [ @@ -25,15 +25,15 @@ "quarto_report.qmd": "e60a379de892055748e4597f9d8c656c" }, "versions": [ - "versions.yml:md5,c3e7ebc433dcacf3d15e1113fd44f5ec" + "versions.yml:md5,ab1c484af3dc5362a395914456c42569" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "24.10.6" }, - "timestamp": "2025-04-22T09:04:23.56469" + "timestamp": "2025-10-20T11:23:11.471279" }, "vuegen - directory (PDF report)": { "content": [ @@ -44,15 +44,15 @@ "quarto_report.qmd": "c447088ca2a435acf926ec5e95c51265" }, "versions": [ - "versions.yml:md5,c3e7ebc433dcacf3d15e1113fd44f5ec" + "versions.yml:md5,ab1c484af3dc5362a395914456c42569" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "24.10.6" }, - "timestamp": "2025-04-22T09:05:54.139709" + "timestamp": "2025-10-20T11:23:52.699959" }, "vuegen - directory (Streamlit report)": { "content": [ @@ -66,7 +66,7 @@ "Static_Plots.py": "ae9c2e46ae9a9e0e5e98fcce87cd7f80" }, "versions": [ - "versions.yml:md5,c3e7ebc433dcacf3d15e1113fd44f5ec" + "versions.yml:md5,ab1c484af3dc5362a395914456c42569" ] } ], @@ -74,6 +74,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.6" }, - "timestamp": "2025-10-16T15:32:46.503388" + "timestamp": "2025-10-20T11:22:39.804459" } } \ No newline at end of file From 9b17dc06e5163779ddda1052610df990771296a9 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Mon, 20 Oct 2025 13:59:50 +0200 Subject: [PATCH 04/12] :art: display versions.yml content in snapshots --- modules/nf-core/vuegen/tests/main.nf.test | 10 ++--- .../nf-core/vuegen/tests/main.nf.test.snap | 40 +++++++++++-------- 2 files changed, 29 insertions(+), 21 deletions(-) diff --git a/modules/nf-core/vuegen/tests/main.nf.test b/modules/nf-core/vuegen/tests/main.nf.test index 48550271b466..40f7c7938f28 100644 --- a/modules/nf-core/vuegen/tests/main.nf.test +++ b/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() } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/vuegen/tests/main.nf.test.snap b/modules/nf-core/vuegen/tests/main.nf.test.snap index 4b31649c8c8f..ea03a715d364 100644 --- a/modules/nf-core/vuegen/tests/main.nf.test.snap +++ b/modules/nf-core/vuegen/tests/main.nf.test.snap @@ -2,9 +2,11 @@ "vuegen - directory (HTML report) -stub": { "content": [ { - "versions": [ - "versions.yml:md5,ab1c484af3dc5362a395914456c42569" - ] + "versions": { + "VUEGEN": { + "vuegen": "0.5.1" + } + } }, [ "report" @@ -14,7 +16,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.6" }, - "timestamp": "2025-10-20T11:23:58.208613" + "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,ab1c484af3dc5362a395914456c42569" - ] + "versions": { + "VUEGEN": { + "vuegen": "0.5.1" + } + } } ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.6" }, - "timestamp": "2025-10-20T11:23:11.471279" + "timestamp": "2025-10-20T13:24:59.558083" }, "vuegen - directory (PDF report)": { "content": [ @@ -43,16 +47,18 @@ "quarto_report.pdf": true, "quarto_report.qmd": "c447088ca2a435acf926ec5e95c51265" }, - "versions": [ - "versions.yml:md5,ab1c484af3dc5362a395914456c42569" - ] + "versions": { + "VUEGEN": { + "vuegen": "0.5.1" + } + } } ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.6" }, - "timestamp": "2025-10-20T11:23:52.699959" + "timestamp": "2025-10-20T13:25:37.140787" }, "vuegen - directory (Streamlit report)": { "content": [ @@ -65,15 +71,17 @@ "Interactive_Plots.py": "4857dc511178812e93c2037c8bbe04f4", "Static_Plots.py": "ae9c2e46ae9a9e0e5e98fcce87cd7f80" }, - "versions": [ - "versions.yml:md5,ab1c484af3dc5362a395914456c42569" - ] + "versions": { + "VUEGEN": { + "vuegen": "0.5.1" + } + } } ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.6" }, - "timestamp": "2025-10-20T11:22:39.804459" + "timestamp": "2025-10-20T13:19:47.56244" } } \ No newline at end of file From b8e8add218b02abcb793a4c324c5b1e4762ffb2d Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Wed, 22 Oct 2025 15:21:33 +0200 Subject: [PATCH 05/12] =?UTF-8?q?=F0=9F=94=A7=20add=20Dockerfile=20to=20in?= =?UTF-8?q?stall=20lastet=20PyPI=20vuegen=20version?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - does not pass hadolint(er) as of now --- modules/nf-core/vuegen/Dockerfile | 45 +++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 modules/nf-core/vuegen/Dockerfile diff --git a/modules/nf-core/vuegen/Dockerfile b/modules/nf-core/vuegen/Dockerfile new file mode 100644 index 000000000000..26c761f6e9ce --- /dev/null +++ b/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 From 6bf04c9b3d86a56607261ccbb171147a89bd0a34 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Wed, 22 Oct 2025 16:49:56 +0200 Subject: [PATCH 06/12] =?UTF-8?q?=F0=9F=9A=A7=20add=20wave=20containers?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- modules/nf-core/vuegen/README.md | 27 +++++++++++++++++++++++++++ modules/nf-core/vuegen/main.nf | 4 +++- 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 modules/nf-core/vuegen/README.md diff --git a/modules/nf-core/vuegen/README.md b/modules/nf-core/vuegen/README.md new file mode 100644 index 000000000000..498bdeb63ed7 --- /dev/null +++ b/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 ` use `apt-get install =` +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 ${..}, array, or is it missing quoting? +Dockerfile:31 DL4006 warning: Set the SHELL option -o pipefail before RUN with a pipe in it. If you are using /bin/sh in an alpine image or if your shell is symlinked to busybox then consider explicitly setting your SHELL to /bin/ash, or disable this check +``` diff --git a/modules/nf-core/vuegen/main.nf b/modules/nf-core/vuegen/main.nf index 53e8156a1e6d..c0ec5dd1dd7d 100644 --- a/modules/nf-core/vuegen/main.nf +++ b/modules/nf-core/vuegen/main.nf @@ -1,7 +1,9 @@ process VUEGEN { label 'process_single' conda "${moduleDir}/environment.yml" - container "dtu_biosustain_dsp/vuegen:v0.5.1-nextflow" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'oras://community.wave.seqera.io/library/vuegen_python:1adb57ecbfa02088' + : 'community.wave.seqera.io/library/vuegen_python:236414fc5cfce774'}" input: val input_type From 9fe09f622f8ab2dcf36ea21d5e8249d3abe597d6 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Fri, 24 Oct 2025 10:21:41 +0200 Subject: [PATCH 07/12] :fire: remove README again --- modules/nf-core/vuegen/README.md | 27 --------------------------- 1 file changed, 27 deletions(-) delete mode 100644 modules/nf-core/vuegen/README.md diff --git a/modules/nf-core/vuegen/README.md b/modules/nf-core/vuegen/README.md deleted file mode 100644 index 498bdeb63ed7..000000000000 --- a/modules/nf-core/vuegen/README.md +++ /dev/null @@ -1,27 +0,0 @@ -# VueGen module - -## Images using wave - -Cached images for 0.5.1 version available on wave, see -[docs](https://docs.seqera.io/wave#seqera-containers---the-community-container-registry) - -platform | version | image --------- | ------- | ----- -docker | linux/amd64 | community.wave.seqera.io/library/vuegen_python:236414fc5cfce774 -singularity | linux/amd64 | oras://community.wave.seqera.io/library/vuegen_python:1adb57ecbfa02088 -docker | linux/arm64 | community.wave.seqera.io/library/vuegen_python:a1dc6490f5045706 -singularity | linux/arm64 | oras://community.wave.seqera.io/library/vuegen_python:64670fcadedf151f - -## Custom docker file - -- check Docker best practices with hadolint, see - [docker-docs](https://docs.docker.com/build/building/best-practices/) - - -```bash -$ hadolint Dockerfile -Dockerfile:7 DL3008 warning: Pin versions in apt get install. Instead of `apt-get install ` use `apt-get install =` -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 -``` From 3493280866c49561cdf0a0ea2530b5dd40a2c910 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Fri, 24 Oct 2025 11:57:38 +0200 Subject: [PATCH 08/12] :fire: remove Dockerfile again --- modules/nf-core/vuegen/Dockerfile | 45 ------------------------------- 1 file changed, 45 deletions(-) delete mode 100644 modules/nf-core/vuegen/Dockerfile diff --git a/modules/nf-core/vuegen/Dockerfile b/modules/nf-core/vuegen/Dockerfile deleted file mode 100644 index 26c761f6e9ce..000000000000 --- a/modules/nf-core/vuegen/Dockerfile +++ /dev/null @@ -1,45 +0,0 @@ -# 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 From f25c41661ed4ebf03027b7a98844cf4980a466bd Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Tue, 28 Oct 2025 16:32:01 +0100 Subject: [PATCH 09/12] =?UTF-8?q?=F0=9F=9A=A7=20try=20to=20follow=20Mahesh?= =?UTF-8?q?'s=20advice?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- modules/nf-core/vuegen/main.nf | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/modules/nf-core/vuegen/main.nf b/modules/nf-core/vuegen/main.nf index c0ec5dd1dd7d..6799ada3964b 100644 --- a/modules/nf-core/vuegen/main.nf +++ b/modules/nf-core/vuegen/main.nf @@ -20,6 +20,15 @@ process VUEGEN { script: def args = task.ext.args ?: '' """ + # Fix Quarto for apptainer + # 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 [[ "${task.conda}" != "null" ]]; then QUARTO_CHECK_FLAG="--quarto_checks" From f71f78c204f5fddb2b56882f00e5180558c24edc Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Wed, 29 Oct 2025 11:18:23 +0100 Subject: [PATCH 10/12] :bug: add explicit cache directory --- modules/nf-core/vuegen/main.nf | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/vuegen/main.nf b/modules/nf-core/vuegen/main.nf index 6799ada3964b..b133e110c969 100644 --- a/modules/nf-core/vuegen/main.nf +++ b/modules/nf-core/vuegen/main.nf @@ -20,7 +20,11 @@ process VUEGEN { script: def args = task.ext.args ?: '' """ - # Fix Quarto for apptainer + # Set environment variables needed for Quarto rendering + # (needed for apptainer/singularity) + export XDG_CACHE_HOME="./.xdg_cache_home" + export XDG_DATA_HOME="./.xdg_data_home" + # Fix Quarto for apptainer: activate conda environment # https://github.com/mahesh-panchal/quarto-docker-singularity-problem ENV_QUARTO="\${ENV_QUARTO:-/opt/conda/etc/conda/activate.d/quarto.sh}" set +u @@ -28,7 +32,7 @@ process VUEGEN { source "\${ENV_QUARTO}" fi set -u - + # Validate quarto_check flag if using a conda environment if [[ "${task.conda}" != "null" ]]; then QUARTO_CHECK_FLAG="--quarto_checks" From 2791af4d7b5462c36fb3ab56c64882809cf6b967 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Wed, 29 Oct 2025 12:05:48 +0100 Subject: [PATCH 11/12] =?UTF-8?q?=F0=9F=94=A7=20bump=20to=20Python=203.12?= =?UTF-8?q?=20and=20remove=20channel=20prefix?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- modules/nf-core/vuegen/environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/vuegen/environment.yml b/modules/nf-core/vuegen/environment.yml index b007e4c77c6d..6dee2d2d963d 100644 --- a/modules/nf-core/vuegen/environment.yml +++ b/modules/nf-core/vuegen/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - conda-forge dependencies: - - bioconda::vuegen=0.5.1 - - python=3.11 + - python=3.12 + - vuegen=0.5.1 From 58ef775f7dd10e7a9999de83151d16636e1a9d68 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Wed, 29 Oct 2025 12:06:22 +0100 Subject: [PATCH 12/12] :wrench: specify singularity image with https ... as specified in the docs: https://nf-co.re/docs/tutorials/nf-core_components/using_seqera_containers --- modules/nf-core/vuegen/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/vuegen/main.nf b/modules/nf-core/vuegen/main.nf index b133e110c969..aae6b6464352 100644 --- a/modules/nf-core/vuegen/main.nf +++ b/modules/nf-core/vuegen/main.nf @@ -2,7 +2,7 @@ process VUEGEN { label 'process_single' conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'oras://community.wave.seqera.io/library/vuegen_python:1adb57ecbfa02088' + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fa/fadd4c6459b24fc3964d47d72dbf809e425054e08f1aec9d56c8bec40b4b3a47/data' : 'community.wave.seqera.io/library/vuegen_python:236414fc5cfce774'}" input: