chore(deps): update condaforge/mambaforge docker tag to v24.9.2

.github/workflows/wave.yml

@@ -21,7 +21,7 @@ jobs:
     if: github.event.pull_request.head.repo.full_name == github.repository
     outputs:
       conda-matrix: ${{ steps.conda-diff.outputs.all_changed_files }}
-      docker-matrix: ${{ steps.docker-diff.outputs.all_changed_files }}
+      dockerfile-matrix: ${{ steps.docker-diff.outputs.all_changed_files }}
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
@@ -48,7 +48,7 @@ jobs:
     # if: github.repository == 'nf-core/modules'
     if: ${{ needs.generate-matrix.outputs.conda-matrix != '[]' }}
     needs: generate-matrix
-    name: Build Conda-based ${{ matrix.profile }} Container
+    name: Build ${{ matrix.profile }} ${{ matrix.platform }} Container
     runs-on: ubuntu-latest
     timeout-minutes: 60
     strategy:
@@ -57,6 +57,7 @@ jobs:
       matrix:
         files: "${{ fromJson(needs.generate-matrix.outputs.conda-matrix) }}"
         profile: [docker, singularity]
+        platform: ["linux/amd64", "linux/arm64"]
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
@@ -76,23 +77,27 @@ jobs:
               $PROFILE \
               --freeze \
               --await \
+              --platform ${{ matrix.platform }} \
               --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
               --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}
 
-  docker-wave:
+  dockerfile-wave:
     # NOTE This should get skipped because generate-matrix won't run
     # if: github.repository == 'nf-core/modules'
-    if: ${{ needs.generate-matrix.outputs.docker-matrix != '[]' }}
+    if: ${{ needs.generate-matrix.outputs.dockerfile-matrix != '[]' }}
     needs: generate-matrix
-    name: Build Dockerfile-based ${{ matrix.profile }} Container
+    name: Build ${{ matrix.profile }} ${{ matrix.platform }} Container
     runs-on: ubuntu-latest
     timeout-minutes: 60
     strategy:
       fail-fast: false
       max-parallel: 4
       matrix:
-        files: "${{ fromJson(needs.generate-matrix.outputs.docker-matrix) }}"
-        profile: [docker, singularity]
+        files: "${{ fromJson(needs.generate-matrix.outputs.dockerfile-matrix) }}"
+        # NOTE singularity build requires a Singularity definition file in place of Dockerfile
+        # https://nextflow.slack.com/archives/C0477AS31T5/p1731755350230149?thread_ts=1731697852.661849&cid=C0477AS31T5
+        profile: [docker]
+        platform: ["linux/amd64", "linux/arm64"]
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
@@ -113,15 +118,13 @@ jobs:
       - name: Build ${{ matrix.profile }} container
         # NOTE If you're changing a Dockerfile and this is running, try to update the Dockerfile to build with wave
         continue-on-error: false
-        env:
-          PROFILE: ${{ (contains(matrix.profile, 'singularity') && '--singularity') || '' }}
         run: |
           wave -f "${{ matrix.files }}" \
-              $PROFILE \
               --freeze \
               --await \
+              --platform ${{ matrix.platform }} \
               --build-repo quay.io/nf-core/modules/${{steps.registry-name.outputs.result}} \
-              --cache-repository quay.io/nf-core/wave-cache \
+              --cache-repository quay.io/nf-core/wave-cache/${{ matrix.profile }}/${{ matrix.platform }} \
               --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
               --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}
 

modules/nf-core/quartonotebook/Dockerfile

@@ -1,25 +1,17 @@
-#
-# First stage: Quarto installation
-#
-FROM ubuntu:24.04 as quarto
+FROM condaforge/mambaforge:24.9.2-0
+#@sha256:e4edd160d0a10c6f577b127021d853b460e7e8c1bf1850c9aa4a52c4b8d9c8ee
 ARG QUARTO_VERSION=1.3.433
 ARG TARGETARCH
-RUN apt-get update \
-    && apt-get install -y --no-install-recommends \
-        ca-certificates \
-        curl \
-    && apt-get clean
 
-RUN mkdir -p /opt/quarto \
-    && curl -o quarto.tar.gz -L "https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-${TARGETARCH}.tar.gz" \
-    && tar -zxvf quarto.tar.gz -C /opt/quarto/ --strip-components=1 \
-    && rm quarto.tar.gz
+LABEL org.opencontainers.image.authors="Erik Fasterius"
+LABEL org.opencontainers.image.description="Dockerfile for the quartonotebook nf-core module"
+LABEL org.opencontainers.image.version="$QUARTO_VERSION"
+LABEL org.opencontainers.image.documentation="https://github.com/nf-core/modules/blob/master/modules/nf-core/quartonotebook/README.md"
+LABEL org.opencontainers.image.source="https://github.com/nf-core/modules"
+LABEL org.opencontainers.image.vendor="nf-core"
+LABEL org.opencontainers.image.license="https://github.com/nf-core/modules/blob/master/LICENSE"
 
-#
-# Second stage: Conda environment
-#
-FROM condaforge/mambaforge:24.1.2-0@sha256:64c45c1a743737f61cf201f54cae974b5c853be94f9c1a84f5e82e0e854f0407
-COPY --from=quarto /opt/quarto /opt/quarto
+ADD https://github.com/quarto-dev/quarto-cli#v${QUARTO_VERSION} /opt/quarto
 ENV PATH="${PATH}:/opt/quarto/bin"
 
 # Install packages using Mamba; also remove static libraries, python bytecode
@@ -32,7 +24,3 @@ RUN mamba env update --name base --file environment.yml \
     && find /opt/conda -follow -type f -name '*.js.map' -delete
 
 CMD /bin/bash
-
-LABEL \
-    authors = "Erik Fasterius" \
-    description = "Dockerfile for the quartonotebook nf-core module"

modules/nf-core/quartonotebook/environment.yml

@@ -1,9 +1,15 @@
 channels:
   - conda-forge
   - bioconda
-
 dependencies:
+  # renovate: datasource=conda depName=conda-forge/quarto
+  # FIXME https://github.com/nf-core/modules/issues/7006
+  - conda-forge::quarto=1.5.57
+  # renovate: datasource=conda depName=conda-forge/jupyter
   - conda-forge::jupyter=1.0.0
+  # renovate: datasource=conda depName=conda-forge/matplotlib
   - conda-forge::matplotlib=3.4.3
+  # renovate: datasource=conda depName=conda-forge/papermill
   - conda-forge::papermill=2.4.0
+  # renovate: datasource=conda depName=conda-forge/r-rmarkdown
   - conda-forge::r-rmarkdown=2.25

modules/nf-core/quartonotebook/main.nf

@@ -1,14 +1,20 @@
-include { dumpParamsYaml; indentCodeBlock } from "./parametrize"
+include {
+    dumpParamsYaml ;
+    indentCodeBlock
+} from "./parametrize"
 
+// NB: You'll likely want to override this with a container containing all
+// required dependencies for your analyses. Or use wave to build the container
+// for you from the environment.yml You'll at least need Quarto itself,
+// Papermill and whatever language you are running your analyses on; you can see
+// an example in this module's Dockerfile.
 process QUARTONOTEBOOK {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
-
-    // NB: You'll likely want to override this with a container containing all
-    // required dependencies for your analyses. You'll at least need Quarto
-    // itself, Papermill and whatever language you are running your analyses on;
-    // you can see an example in this module's Dockerfile.
-    container "docker.io/erikfas/quartonotebook"
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/25/25d0a9decefd5d369b8f9b8c934640bd61493df2c95c39b0c580e765e0d2a644/data'
+        : 'community.wave.seqera.io/library/quarto_jupyter_matplotlib_papermill_r-rmarkdown:95c6620495eabcd1'}"
 
     input:
     tuple val(meta), path(notebook)
@@ -17,29 +23,33 @@ process QUARTONOTEBOOK {
     path extensions
 
     output:
-    tuple val(meta), path("*.html")     , emit: html
+    tuple val(meta), path("*.html"), emit: html
     tuple val(meta), path("${notebook}"), emit: notebook
     tuple val(meta), path("artifacts/*"), emit: artifacts, optional: true
-    tuple val(meta), path("params.yml") , emit: params_yaml, optional: true
+    tuple val(meta), path("params.yml"), emit: params_yaml, optional: true
     tuple val(meta), path("_extensions"), emit: extensions, optional: true
-    path "versions.yml"                 , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    // Exit if running this module with -profile conda / -profile mamba
+    // FIXME https://github.com/nf-core/modules/issues/7006
+    // Exit if running this module with -profile conda / -profile mamba on ARM64
     // This is because of issues with getting a homogenous environment across
     // both AMD64 and ARM64 architectures; please find more information at
     // https://github.com/nf-core/modules/pull/4876#discussion_r1483541037.
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "The QUARTONOTEBOOK module does not support Conda/Mamba, please use Docker / Singularity / Podman instead."
+        arch = System.getProperty("os.arch")
+        if (arch == "arm64" || arch == "aarch64") {
+            exit(1, "The QUARTONOTEBOOK module does not support Conda/Mamba on ARM64. Please use Docker / Singularity / Podman instead.")
+        }
     }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def parametrize = (task.ext.parametrize == null) ?  true : task.ext.parametrize
-    def implicit_params = (task.ext.implicit_params == null) ? true : task.ext.implicit_params
-    def meta_params = (task.ext.meta_params == null) ? true : task.ext.meta_params
+    def parametrize = task.ext.parametrize == null ? true : task.ext.parametrize
+    def implicit_params = task.ext.implicit_params == null ? true : task.ext.implicit_params
+    def meta_params = task.ext.meta_params == null ? true : task.ext.meta_params
 
     // Dump parameters to yaml file.
     // Using a YAML file over using the CLI params because
@@ -74,10 +84,10 @@ process QUARTONOTEBOOK {
     export XDG_DATA_HOME="./.xdg_data_home"
 
     # Set parallelism for BLAS/MKL etc. to avoid over-booking of resources
-    export MKL_NUM_THREADS="$task.cpus"
-    export OPENBLAS_NUM_THREADS="$task.cpus"
-    export OMP_NUM_THREADS="$task.cpus"
-    export NUMBA_NUM_THREADS="$task.cpus"
+    export MKL_NUM_THREADS="${task.cpus}"
+    export OPENBLAS_NUM_THREADS="${task.cpus}"
+    export OMP_NUM_THREADS="${task.cpus}"
+    export NUMBA_NUM_THREADS="${task.cpus}"
 
     # Render notebook
     quarto render \\

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

@@ -57,11 +57,11 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
                     process.out.artifacts,
                     process.out.params_yaml,
+                    path(process.out.versions.get(0)).yaml,
                 ).match() },
-                { assert path(process.out.html[0][1]).readLines().any { it.contains('Hello world') } }
+                { assert path(process.out.html[0][1]).readLines().any { it.contains('Hello world') } },
             )
         }
 
@@ -116,11 +116,11 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
                     process.out.artifacts,
                     process.out.params_yaml,
+                    path(process.out.versions.get(0)).yaml,
                 ).match() },
-                { assert path(process.out.html[0][1]).readLines().any { it.contains('Hello world') } }
+                { assert path(process.out.html[0][1]).readLines().any { it.contains('Hello world') } },
             )
         }