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CaroAMNmashehu
CaroAMN
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mashehu
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new module numorph-3dunet (#12130)
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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‎.github/skip_nf_test.json‎

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{
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"conda": [
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"modules/nf-core/numorph/3dunet",
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"modules/nf-core/numorph/intensity",
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"modules/nf-core/numorph/resample",
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"modules/nf-core/mat2json",
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"subworkflows/nf-core/deepvariant/tests/equality"
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],
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"singularity": [
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"modules/nf-core/numorph/3dunet",
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"modules/nf-core/bases2fastq",
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"modules/nf-core/deepsomatic",
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"modules/nf-core/deepvariant/rundeepvariant",

‎modules/nf-core/numorph/3dunet/Dockerfile‎

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## optimized nvidia base container for older python and tensorflow
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FROM nvcr.io/nvidia/tensorflow:20.10-tf1-py3
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ARG NUMORPH_3DUNET_VERSION="1.0.9"
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LABEL org.opencontainers.image.authors=="Carolin Schwitalla <carolin.schwitalla@uni-tuebingen.de>"
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LABEL org.opencontainers.image.description="Docker image for the NuMorph 3D-UNet to perform nuclei quantification on light-sheet microscopy data"
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LABEL org.opencontainers.image.licenses="MIT"
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LABEL org.opencontainers.image.version="$NUMORPH_3DUNET_VERSION"
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RUN apt-get update && apt-get install -y --no-install-recommends \
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git \
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libgl1-mesa-glx \
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libglib2.0-0 \
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libsm6 \
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libxext6 \
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libxrender-dev \
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&& rm -rf /var/lib/apt/lists/*
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RUN pip install --upgrade pip
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# the tool needs this
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RUN pip install git+https://github.com/keras-team/keras-contrib.git
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# Install the package
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RUN pip install numorph-3dunet==$NUMORPH_3DUNET_VERSION
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# Create directory for models
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RUN mkdir -p /models
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CMD ["/bin/bash"]

‎modules/nf-core/numorph/3dunet/README.md‎

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# Updating the docker container and making a new module release
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To update this tool :
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2. Edit the Dockerfile in the following lines:
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```diff
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- ARG NUMORPH_PREPROCESSING_VERSION="1.0.0"
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+ ARG NUMORPH_PREPROCESSING_VERSION="<New version>"
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```
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3. Open a PR against [nf-core/modules](https://github.com/nf-core/modules) directly, push the changes, and the Dockerfile should be built and uploaded to `quay.io/nf-core/numorph-3dunet`!

‎modules/nf-core/numorph/3dunet/main.nf‎

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process NUMORPH_3DUNET {
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tag "$meta.id"
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label 'process_gpu'
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container "quay.io/nf-core/numorph-3dunet:1.0.9"
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input:
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tuple val(meta), path(img_directory), path(parameter_file)
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path(model_file)
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output:
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tuple val(meta), path("${prefix}/") , emit: cellcounts
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tuple val("${task.process}"), val('numorph_3dunet'), eval('numorph_3dunet --version'), emit: versions_numorph_3dunet, topic: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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echo "Checking GPU access:"
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nvidia-smi
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mkdir -p ${prefix}
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img_dir=\$(readlink -f ${img_directory})
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numorph_3dunet \\
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-i \$img_dir \\
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-o ${prefix} \\
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--model_file ${model_file} \\
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--sample_id ${prefix} \\
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$args
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"""
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stub:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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mkdir -p ${prefix}
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touch ${prefix}/${prefix}.csv
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touch ${prefix}/${prefix}_counts.csv
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"""
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}

‎modules/nf-core/numorph/3dunet/meta.yml‎

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name: "numorph_3dunet"
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description: "3DUnet for cell nuclei quantification on 3D microscopy images of the
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numorph toolkit."
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keywords:
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- segmentation
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- cell nuclei
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- light-sheet microscopy
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- numorph
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tools:
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- "numorph_3dunet":
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description: "This package contains the original 3DUnet for cell nuclei quantification
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on 3D microscopy images of the numorph toolkit."
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homepage: "https://github.com/qbic-pipelines/numorph_3dunet"
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documentation: "https://github.com/qbic-pipelines/numorph_3dunet"
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tool_dev_url: "https://github.com/qbic-pipelines/numorph_3dunet"
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licence:
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- "MIT"
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identifier: ""
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- img_directory:
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type: directory
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description: Directory containing stitched image files
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pattern: "*.{tif,tiff}"
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ontologies:
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- edam: "http://edamontology.org/format_3591"
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- edam: "http://edamontology.org/format_3727"
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- parameter_file:
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type: file
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description: File containing parameters for numorph tools
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pattern: "*.{csv}"
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ontologies:
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- edam: "http://edamontology.org/format_3752"
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- model_file:
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type: file
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description: File containing the trained model
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pattern: "*.{h5}"
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ontologies:
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- edam: "http://edamontology.org/format_3590"
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output:
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cellcounts:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- ${prefix}/:
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type: directory
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description: Directory containing cell count results
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pattern: "${meta.id}/"
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versions_numorph_3dunet:
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- - ${task.process}:
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type: string
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description: The name of the process
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- numorph_3dunet:
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type: string
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description: The name of the tool
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- "numorph_3dunet --version":
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type: eval
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description: The expression to obtain the version of the tool
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topics:
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versions:
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- - "${task.process}":
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type: string
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description: The name of the process
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- "numorph_3dunet":
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type: string
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description: The name of the tool
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- "numorph_3dunet --version":
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type: eval
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description: The expression to obtain the version of the tool
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authors:
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- "@CaroAMN"
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maintainers:
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- "@CaroAMN"

‎modules/nf-core/numorph/3dunet/tests/main.nf.test‎

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// nf-core modules test numorph/3dunet
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nextflow_process {
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name "Test Process NUMORPH_3DUNET"
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script "../main.nf"
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process "NUMORPH_3DUNET"
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tag "modules"
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tag "modules_nfcore"
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tag "numorph"
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tag "numorph/3dunet"
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tag "unzip"
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tag "gpu"
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test("numorph-3DUnet test - tif") {
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setup {
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run ("UNZIP") {
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script "../../../unzip/main.nf"
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process {
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"""
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input[0] = Channel.fromList([
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tuple([ id:'TEST1'],
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file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/lsmquant/test_data/unet_test_images.zip'))
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])
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"""
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}
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}
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}
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when {
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params {
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outdir = "$outputDir"
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}
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process {
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"""
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input[0] = UNZIP.out.unzipped_archive.map { meta, unzipped_archive ->
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def image_dir = file(unzipped_archive).listFiles().find { it.isDirectory() }
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tuple(
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meta,
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image_dir ?: unzipped_archive,
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file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/lsmquant/test_data/parameterfiles/params_TEST1_lsmquant.csv'))
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}
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input[1] = file('https://zenodo.org/records/16893708/files/075_121_model.h5')
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"""
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}
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}
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then {
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def cellcounDir = process.out.cellcounts.get(0).get(1)
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def cellcountFiles = getAllFilesFromDir(cellcounDir, relative: true, includeDir: false)
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assertAll(
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{assert process.success },
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{assert cellcountFiles.size() == 2 },
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{ assert snapshot(
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cellcountFiles,
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process.out.findAll { key, val -> key.startsWith('versions') }
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).match() }
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)
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}
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}
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test("numorph-3DUnet stub test - tif") {
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options '-stub'
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when {
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process {
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"""
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input[0] = Channel.fromList([
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tuple([ id:'TEST1'],
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file('https://zenodo.org/records/14916478/files/ctip2_topro.zip'),
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file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/lsmquant/test_data/parameterfiles/params_TEST1_lsmquant.csv'))
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])
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input[1] = file('https://zenodo.org/records/16893708/files/075_121_model.h5')
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(sanitizeOutput(process.out)).match() }
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)
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}
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}
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}

‎modules/nf-core/numorph/3dunet/tests/main.nf.test.snap‎

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{
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"numorph-3DUnet test - tif": {
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"content": [
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[
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"TEST1.csv",
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"TEST1_counts.csv"
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],
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{
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"versions_numorph_3dunet": [
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[
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"NUMORPH_3DUNET",
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"numorph_3dunet",
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"1.0.9"
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]
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]
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}
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],
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"timestamp": "2026-06-23T14:16:39.850891617",
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"meta": {
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"nf-test": "0.9.4",
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"nextflow": "25.10.4"
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}
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},
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"numorph-3DUnet stub test - tif": {
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"content": [
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{
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"cellcounts": [
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[
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{
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"id": "TEST1"
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},
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[
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"TEST1.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
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"TEST1_counts.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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]
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],
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"versions_numorph_3dunet": [
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[
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"NUMORPH_3DUNET",
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"numorph_3dunet",
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"1.0.9"
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]
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]
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}
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],
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"timestamp": "2026-06-26T13:59:27.663751068",
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"meta": {
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"nf-test": "0.9.4",
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"nextflow": "25.10.4"
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}
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}
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}

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