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Merge pull request #3872 from nf-core/dev
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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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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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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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FROM mcr.microsoft.com/devcontainers/base:2.0.2-debian12@sha256:23fa69fed758b7927c60061317d73baf7d66b9fca5c344e80bce3a940b229af0 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

‎.devcontainer/setup.sh‎

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# Update Nextflow
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nextflow self-update
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# Install specifically the version of tools from the workspace
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pip install --upgrade -r requirements.txt -r requirements-dev.txt -e .
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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/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 `.devcontainer/devcontainer.json` 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`.
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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. 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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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`.
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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`.

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

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- name: Upload log file artifact
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if: ${{ always() }}
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uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
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uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
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with:
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name: nf-core-log-file-${{ matrix.NXF_VER }}
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path: create-lint-wf/log.txt

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

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"multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
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‎.github/snapshots/changelog.nf.test.snap‎

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‎.github/snapshots/ci.nf.test.snap‎

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

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

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

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