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Merge pull request #3833 from nf-core/dev
dev > main for 3.4.0 release
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‎.devcontainer/build-devcontainer/Dockerfile‎

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# devcontainers/miniconda image based on debian (bookworm)
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# see tags and images: https://mcr.microsoft.com/en-us/artifact/mar/devcontainers/miniconda/tags
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FROM "mcr.microsoft.com/devcontainers/miniconda@sha256:8e262a2664fab1d53054738d3633338558a2078ce66d3abde55c130f0d5da94f" AS build
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# copy this repo at current revision
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COPY . /root/nfcore-tools/
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# Explicitly reinstall python 3.13 via conda
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# install local nf-core tools version, and precommit hooks
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RUN cd /root/nfcore-tools/ && \
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conda install -y python=3.13 && \
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pip install --no-cache-dir --upgrade pip setuptools wheel pre-commit && \
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pip install -r requirements.txt --no-cache-dir -e . && \
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pre-commit install --install-hooks && \
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rm -rf /root/.cache/pip
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# Install nextflow and nf-test via conda and run conda clean
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RUN conda install -c bioconda -y nextflow nf-test && \
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conda clean -afy
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# Install dependencies for apptainer build and apptainer and run apt clean
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RUN apt-get update --quiet && \
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apt-get install -y curl rpm2cpio cpio && \
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curl -s https://raw.githubusercontent.com/apptainer/apptainer/main/tools/install-unprivileged.sh | bash -s - /usr/local/apptainer && \
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echo "PATH=/usr/local/apptainer/bin:$PATH" >> $HOME/.bashrc && \
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apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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# Final stage to copy only the required files after installation
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FROM "mcr.microsoft.com/devcontainers/base:debian@sha256:ce2e9e611939e611b737362c045bb6d3449bb3efb84898525d724aace1737b90" AS final
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# Copy only the conda environment and site-packages from build stage
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COPY --from=build /opt/conda /opt/conda
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COPY --from=build /root/nfcore-tools/nf_core /root/nfcore-tools/nf_core
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# Copy aptainer install from build stage
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COPY --from=build /usr/local/apptainer /usr/local/apptainer
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COPY --from=build /root/.bashrc /root/.bashrc

‎.devcontainer/build-devcontainer/devcontainer.json‎

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{
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"name": "nfcore-devcontainer-build",
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// installs python3.14, nf-core tools from current workspace, nextflow, nf-test,
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// and apptainer based on mcr.microsoft.com/devcontainers/miniconda image
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"build": {
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"dockerfile": "./Dockerfile",
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"context": "../.."
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},
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"features": {
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"ghcr.io/devcontainers/features/docker-outside-of-docker:1.6.3": {}
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},
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"remoteEnv": {
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"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
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},
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"remoteUser": "root",
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"privileged": true,
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// Configure tool-specific properties.
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"customizations": {
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// Configure properties specific to VS Code.
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"vscode": {
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// Set *default* container specific settings.json values on container create.
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"settings": {
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"python.defaultInterpreterPath": "/opt/conda/bin/python"
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},
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// Add the IDs of extensions you want installed when the container is created.
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"extensions": [
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"charliermarsh.ruff",
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"ms-python.python",
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"ms-python.vscode-pylance",
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"nf-core.nf-core-extensionpack"
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]
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}
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}
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}

‎.devcontainer/devcontainer.json‎

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{
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"name": "nfcore",
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"image": "nfcore/gitpod:latest",
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"postCreateCommand": "python -m pip install --upgrade -r ../requirements-dev.txt -e ../ && pre-commit install --install-hooks",
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"remoteUser": "gitpod",
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"runArgs": ["--privileged"],
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"image": "nfcore/devcontainer:latest",
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// Configure tool-specific properties.
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"customizations": {
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// Configure properties specific to VS Code.
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"vscode": {
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// Set *default* container specific settings.json values on container create.
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"settings": {
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"python.defaultInterpreterPath": "/opt/conda/bin/python"
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},
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"remoteEnv": {
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// Workspace path on the host for mounting with docker-outside-of-docker
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"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
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},
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// Add the IDs of extensions you want installed when the container is created.
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"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
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}
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"onCreateCommand": "./.devcontainer/setup.sh",
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"remoteUser": "root",
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"privileged": true,
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"hostRequirements": {
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"cpus": 4,
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"memory": "16gb",
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"storage": "32gb"
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}
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}

‎.devcontainer/setup.sh‎

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#!/usr/bin/env bash
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# Customise the terminal command prompt
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echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
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echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
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export PROMPT_DIRTRIM=2
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export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
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# Update Nextflow
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nextflow self-update
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# Update welcome message
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echo "Welcome to the nf-core devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

‎.github/ISSUE_TEMPLATE/bug_report.yml‎

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* Executor _(eg. slurm, local, awsbatch)_
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* OS _(eg. CentOS Linux, macOS, Linux Mint)_
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* Version of nf-core/tools _(eg. 1.10, 1.12.1, 1.13)_
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* Python version _(eg. 3.12, 3.13)_
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* Python version _(eg. 3.13, 3.14)_

‎.github/RELEASE_CHECKLIST.md‎

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2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_.
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3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc)
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4. Check that modules/subworkflows in template are up to date with the latest releases
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5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:latest`.
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5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the `.devcontainer/devcontainer.json` container to `nfcore/gitpod:latest`.
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6. Make sure all CI tests are passing!
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7. Create a PR from `dev` to `main`
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8. Make sure all CI tests are passing again (additional tests are run on PRs to `main`)
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9. Request review (2 approvals required)
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10. Merge the PR into `main`
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11. Wait for CI tests on the commit to passed
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12. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
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13. Create a new release copying the `CHANGELOG` for that release into the description section.
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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.
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9. Warn someone from Seqera to make sure that the Seqera Platform is working as expected with the new template: use the `nf-core/testpipeline` new branch with the template updates.
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10. Make sure all CI tests are passing again (additional tests are run on PRs to `main`)
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11. Request review (2 approvals required)
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12. Merge the PR into `main`
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13. Wait for CI tests on the commit to passed
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14. Create a new release copying the `CHANGELOG` for that release into the description section.
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## After release
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1. Check the automated template synchronisation has been triggered properly. This should automatically open PRs directly to individual pipeline repos with the appropriate changes to update the pipeline template.
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2. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
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3. 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)
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4. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:dev`.
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5. Run `rich-codex` on the [tools/website repo](https://github.com/nf-core/website/actions/workflows/rich-codex.yml) to regenerate docs screengrabs (actions `workflow_dispatch` button)
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1. Run the `Sync template` GitHub Action to trigger the template update PR to some selected pipelines (sarek, createtaxdb, proteinfold, mag, #team-maintainers channel) and ask the pipeline maintainers to make the update and report any issues/comments.
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2. Run `rich-codex` to regenerate docs screengrabs: `Generate images for docs` GitHub Action on the [tools/website repo](https://github.com/nf-core/website/actions/workflows/rich-codex.yml).
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3. Manually trigger the `Sync template` GitHub Action for all pipelines.
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4. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
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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)
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6. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` and change the `.devcontainer/devcontainer.json` container to `nfcore/gitpod:dev`.

‎.github/renovate.json5‎

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$schema: "https://docs.renovatebot.com/renovate-schema.json",
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extends: ["github>nf-core/ops//.github/renovate/default.json5"],
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ignorePaths: ["**/nf_core/pipeline-template/modules/nf-core/**"],
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baseBranches: ["dev"],
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baseBranchPatterns: ["dev"],
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packageRules: [
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{
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matchDatasources: ["docker"],

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

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{
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"-profile test": {
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"content": [
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{
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"FASTQC": {
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"fastqc": "0.12.1"
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"fastqc/SAMPLE3_SE_2_fastqc.zip",
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"multiqc",
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"multiqc/multiqc_data",
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"multiqc/multiqc_data/BETA-multiqc.parquet",
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"multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
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"multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
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"multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
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"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
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"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
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"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
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"multiqc/multiqc_data/llms-full.txt",
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"multiqc/multiqc_data/multiqc.log",
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"multiqc/multiqc_data/multiqc.parquet",
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"multiqc/multiqc_data/multiqc_citations.txt",
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]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nf-test": "0.9.3",
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"nextflow": "25.03.1"
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},
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"timestamp": "2025-05-07T13:52:10.350817122"

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

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{
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"-profile test": {
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"FASTQC": {
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"fastqc/SAMPLE3_SE_2_fastqc.zip",
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"multiqc",
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"multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
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"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
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"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
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"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
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"multiqc/multiqc_data/llms-full.txt",
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"multiqc/multiqc_data/multiqc.log",
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"multiqc/multiqc_data/multiqc.parquet",
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]
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.03.1"
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},
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"timestamp": "2025-05-07T13:52:01.993722854"

‎.github/snapshots/ci.nf.test.snap‎

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{
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"fastqc/SAMPLE3_SE_2_fastqc.zip",
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"multiqc",
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"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
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"multiqc/multiqc_data/llms-full.txt",
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"multiqc/multiqc_data/multiqc.parquet",
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.03.1"
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},
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"timestamp": "2025-05-07T13:52:03.306256217"

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