feat(modules): add containers create subcommand

.devcontainer/build-devcontainer/Dockerfile

@@ -1,33 +1,33 @@
 # devcontainers/miniconda image based on debian (bookworm)
 # see tags and images: https://mcr.microsoft.com/en-us/artifact/mar/devcontainers/miniconda/tags
-FROM mcr.microsoft.com/devcontainers/miniconda@sha256:19516babd35bccd1429591a255dd867b2c8c01606cc594a8a6fe5db03309ecf8 AS build
+FROM mcr.microsoft.com/devcontainers/miniconda@sha256:b99720fe7bdce0346dc3c3ff54414ba78ff183d85a5a9d9a2e2e5775ce679347 AS build
 
 # copy this repo at current revision
 COPY . /root/nfcore-tools/
 
 # Explicitly reinstall python 3.13 via conda
-# install local nf-core tools version, and precommit hooks
+# Install uv and local nf-core tools version, and precommit hooks
 RUN cd /root/nfcore-tools/ && \
     conda install -y python=3.13 && \
-    pip install --no-cache-dir --upgrade pip setuptools wheel pre-commit && \
-    pip install -r requirements.txt --no-cache-dir -e . && \
-    pre-commit install --install-hooks && \
-    rm -rf /root/.cache/pip
+    pip install --no-cache-dir --upgrade pip uv && \
+    uv pip install --system --no-cache-dir . && \
+    rm -rf /root/.cache/pip /root/.cache/uv
 
 # Install nextflow and nf-test via conda and run conda clean
 RUN conda install -c bioconda -y nextflow nf-test && \
     conda clean -afy
 
 # Install dependencies for apptainer build and apptainer and run apt clean
-RUN apt-get update --quiet && \
+RUN rm -f /etc/apt/sources.list.d/yarn.list && \
+    apt-get update --quiet && \
     apt-get install -y curl rpm2cpio cpio && \
     curl -s https://raw.githubusercontent.com/apptainer/apptainer/main/tools/install-unprivileged.sh | bash -s - /usr/local/apptainer && \
     echo "PATH=/usr/local/apptainer/bin:$PATH" >> $HOME/.bashrc && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
 # Final stage to copy only the required files after installation
-FROM mcr.microsoft.com/devcontainers/base:debian@sha256:2e826a6ae92e5744cc0a471a03b4411e64f6b7cc6af3adaecddad697f0018f10 AS final
+FROM mcr.microsoft.com/devcontainers/base:2.1.6-debian12@sha256:15143a8c806afb8db57ae2c92876c112d7a6a1ced31cd7aa8b414201782757a4 AS final
 
 # Copy only the conda environment and site-packages from build stage
 COPY --from=build /opt/conda /opt/conda

.devcontainer/build-devcontainer/devcontainer.json

@@ -1,4 +1,5 @@
 {
+    "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json",
     "name": "nfcore-devcontainer-build",
 
     // installs python3.14, nf-core tools from current workspace, nextflow, nf-test,

.devcontainer/devcontainer.json

@@ -1,4 +1,5 @@
 {
+    "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json",
     "name": "nfcore",
     "image": "nfcore/devcontainer:dev",
 

.devcontainer/setup.sh

@@ -10,7 +10,14 @@ export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
 nextflow self-update
 
 # Install specifically the version of tools from the workspace
-pip install --upgrade  -r requirements.txt -r requirements-dev.txt -e .
+uv sync --all-extras
+
+# Activate the virtual environment automatically on login
+echo "source $(pwd)/.venv/bin/activate" >> $HOME/.bashrc
+
+# Install pre-commit hooks (using the venv)
+source .venv/bin/activate
+prek install --install-hooks
 
 # Update welcome message
 echo "Welcome to the nf-core devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

.github/RELEASE_CHECKLIST.md

@@ -4,7 +4,7 @@
 2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_.
 3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc)
 4. Check that modules/subworkflows in template are up to date with the latest releases
-5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py`.
+5. Create a PR to `dev` to bump the version in `CHANGELOG.md`. `pyproject.toml` and in `uv.lock` (by running `uv sync`).
 6. Make sure all CI tests are passing!
 7. Create a PR from `dev` to `main`
 8. Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR: use the `Sync template` GitHub Action from the tools repository specifying the pipeline name and running from the `dev` branch.
@@ -22,4 +22,4 @@
 3. Manually trigger the `Sync template` GitHub Action for all pipelines.
 4. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
 5. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065)
-6. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py`.
+6. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md`, `pyproject.toml` and in `uv.lock` (by running `uv sync`).

.github/actions/create-lint-wf/action.yml

@@ -26,24 +26,30 @@ runs:
       run: |
         mkdir -p create-lint-wf && cd create-lint-wf
         export NXF_WORK=$(pwd)
-        nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
+        uv run nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
 
     # Try syncing it before we change anything
     - name: nf-core pipelines sync
       shell: bash
-      run: nf-core --log-file log.txt pipelines sync --dir nf-core-testpipeline/
+      run: uv run nf-core --log-file log.txt pipelines sync --dir nf-core-testpipeline/
       working-directory: create-lint-wf
-
+    #FIXME debugging
+    - name: check directory
+      shell: bash
+      run: |
+        pwd
+        ls -l
+      working-directory: create-lint-wf/nf-core-testpipeline
     # Run code style linting
     - name: run pre-commit
       shell: bash
-      run: pre-commit run --all-files
+      run: uv run pre-commit run --all-files
       working-directory: create-lint-wf
 
     # Update modules to the latest version
     - name: nf-core modules update
       shell: bash
-      run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview
+      run: uv run nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview
       working-directory: create-lint-wf
 
     # Remove TODO statements
@@ -67,47 +73,47 @@ runs:
     # Run nf-core pipelines linting
     - name: nf-core pipelines lint
       shell: bash
-      run: nf-core --verbose --log-file log.txt --hide-progress pipelines lint --dir nf-core-testpipeline --fail-ignored --fail-warned
+      run: uv run nf-core --verbose --log-file log.txt --hide-progress pipelines lint --dir nf-core-testpipeline --fail-ignored --fail-warned
       working-directory: create-lint-wf
 
     - name: nf-core pipelines bump-version to release
       shell: bash
-      run: nf-core --log-file log.txt pipelines bump-version --dir nf-core-testpipeline/ 1.1
+      run: uv run nf-core --log-file log.txt pipelines bump-version --dir nf-core-testpipeline/ 1.1
       working-directory: create-lint-wf
 
     - name: nf-core pipelines lint in release mode
       shell: bash
-      run: nf-core --log-file log.txt --hide-progress pipelines lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
+      run: uv run nf-core --log-file log.txt --hide-progress pipelines lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
       working-directory: create-lint-wf
 
     - name: Upload log file artifact
       if: ${{ always() }}
-      uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+      uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7
       with:
         name: nf-core-log-file-${{ matrix.NXF_VER }}
         path: create-lint-wf/log.txt
 
     - name: nf-core modules install
       shell: bash
-      run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
+      run: uv run nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
       working-directory: create-lint-wf
 
     - name: nf-core modules install gitlab
       shell: bash
-      run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch branch-tester install fastp --dir nf-core-testpipeline/
+      run: uv run nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch branch-tester install fastp --dir nf-core-testpipeline/
       working-directory: create-lint-wf
 
     - name: nf-core modules list local
       shell: bash
-      run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
+      run: uv run nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
       working-directory: create-lint-wf
 
     - name: nf-core modules list remote
       shell: bash
-      run: nf-core --log-file log.txt modules list remote
+      run: uv run nf-core --log-file log.txt modules list remote
       working-directory: create-lint-wf
 
     - name: nf-core modules list remote gitlab
       shell: bash
-      run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote
+      run: uv run nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote
       working-directory: create-lint-wf

.github/renovate.json5

@@ -13,6 +13,10 @@
             matchDatasources: ["docker"],
             registryUrls: ["docker.io"],
         },
+        {
+            matchCurrentValue: "/</",
+            rangeStrategy: "in-range-only",
+        },
     ],
     gitIgnoredAuthors: ["core@nf-co.re"],
 }

.github/snapshots/adaptivecard.nf.test.snap

@@ -47,6 +47,7 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -59,6 +60,7 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -71,6 +73,7 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",

.github/snapshots/changelog.nf.test.snap

@@ -47,6 +47,7 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -59,6 +60,7 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -71,6 +73,7 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",

.github/snapshots/ci.nf.test.snap

@@ -47,6 +47,7 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -59,6 +60,7 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -71,6 +73,7 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",

.github/snapshots/citations.nf.test.snap

@@ -47,6 +47,7 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -59,6 +60,7 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -71,6 +73,7 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",

.github/snapshots/code_linters.nf.test.snap

@@ -47,6 +47,7 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -59,6 +60,7 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -71,6 +73,7 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",

.github/snapshots/codespaces.nf.test.snap

@@ -47,6 +47,7 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -59,6 +60,7 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -71,6 +73,7 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",