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Merge pull request #71 from nf-core/dev
First pipeline release
2 parents d74ee16 + bf1bee7 commit 382d936

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‎.devcontainer/devcontainer.json‎

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@@ -1,20 +1,20 @@
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{
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"name": "nfcore",
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"image": "nfcore/gitpod:latest",
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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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"remoteUser": "root",
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"privileged": true,
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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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"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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"onCreateCommand": "./.devcontainer/setup.sh",
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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/proteinannotator devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

‎.editorconfig‎

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This file was deleted.

‎.github/CONTRIBUTING.md‎

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@@ -78,7 +78,7 @@ If you wish to contribute a new step, please use the following coding standards:
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5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
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6. Add sanity checks and validation for all relevant parameters.
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7. Perform local tests to validate that the new code works as expected.
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8. If applicable, add a new test command in `.github/workflow/ci.yml`.
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8. If applicable, add a new test in the `tests` directory.
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9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
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10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
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‎.github/PULL_REQUEST_TEMPLATE.md‎

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@@ -18,8 +18,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/prot
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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/proteinannotator/tree/master/.github/CONTRIBUTING.md)
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- [ ] If necessary, also make a PR on the nf-core/proteinannotator _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
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- [ ] Make sure your code lints (`nf-core pipelines lint`).
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- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
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- [ ] Ensure the test suite passes (e.g. `nf-test test */local --profile=~test,docker` for all new local tests).
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- [ ] Check for unexpected warnings in debug mode (`nf-test test */local --profile=~test,docker,debug`).
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- [ ] Usage Documentation in `docs/usage.md` is updated.
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- [ ] Output Documentation in `docs/output.md` is updated.
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- [ ] `CHANGELOG.md` is updated.

‎.github/actions/get-shards/action.yml‎

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name: "Get number of shards"
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description: "Get the number of nf-test shards for the current CI job"
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inputs:
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max_shards:
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description: "Maximum number of shards allowed"
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required: true
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paths:
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description: "Component paths to test"
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required: false
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tags:
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description: "Tags to pass as argument for nf-test --tag parameter"
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required: false
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outputs:
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shard:
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description: "Array of shard numbers"
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value: ${{ steps.shards.outputs.shard }}
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total_shards:
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description: "Total number of shards"
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value: ${{ steps.shards.outputs.total_shards }}
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runs:
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using: "composite"
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steps:
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- name: Install nf-test
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uses: nf-core/setup-nf-test@v1
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with:
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version: ${{ env.NFT_VER }}
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- name: Get number of shards
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id: shards
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shell: bash
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run: |
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# Run nf-test with dynamic parameter
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nftest_output=$(nf-test test \
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--profile +docker \
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$(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
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--dry-run \
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--ci \
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--changed-since HEAD^) || {
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echo "nf-test command failed with exit code $?"
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echo "Full output: $nftest_output"
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exit 1
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}
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echo "nf-test dry-run output: $nftest_output"
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# Default values for shard and total_shards
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shard="[]"
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total_shards=0
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# Check if there are related tests
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if echo "$nftest_output" | grep -q 'No tests to execute'; then
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echo "No related tests found."
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else
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# Extract the number of related tests
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number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p')
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if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then
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shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} ))
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shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .)
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total_shards="$shards_to_run"
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else
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echo "Unexpected output format. Falling back to default values."
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fi
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fi
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# Write to GitHub Actions outputs
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echo "shard=$shard" >> $GITHUB_OUTPUT
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echo "total_shards=$total_shards" >> $GITHUB_OUTPUT
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# Debugging output
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echo "Final shard array: $shard"
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echo "Total number of shards: $total_shards"

‎.github/actions/nf-test/action.yml‎

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name: "nf-test Action"
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description: "Runs nf-test with common setup steps"
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inputs:
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profile:
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description: "Profile to use"
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required: true
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shard:
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description: "Shard number for this CI job"
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required: true
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total_shards:
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description: "Total number of test shards(NOT the total number of matrix jobs)"
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required: true
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paths:
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description: "Test paths"
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required: true
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tags:
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description: "Tags to pass as argument for nf-test --tag parameter"
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required: false
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runs:
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using: "composite"
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steps:
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- name: Print Modules Folder Tree
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uses: jaywcjlove/github-action-folder-tree@main
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with:
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exclude: "node_modules|dist|.git|.husky"
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path: ./modules
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depth: 10
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- name: Print Subworkflows Folder Tree
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uses: jaywcjlove/github-action-folder-tree@main
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with:
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exclude: "node_modules|dist|.git|.husky"
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path: ./subworkflows
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depth: 10
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- name: Setup Nextflow
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uses: nf-core/setup-nextflow@v2
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with:
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version: "${{ env.NXF_VERSION }}"
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- name: Set up Python
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uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
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with:
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python-version: "3.14"
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- name: Install nf-test
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uses: nf-core/setup-nf-test@v1
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with:
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version: "${{ env.NFT_VER }}"
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install-pdiff: true
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- name: Setup apptainer
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if: contains(inputs.profile, 'singularity')
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uses: eWaterCycle/setup-apptainer@main
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- name: Set up Singularity
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if: contains(inputs.profile, 'singularity')
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shell: bash
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run: |
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mkdir -p $NXF_SINGULARITY_CACHEDIR
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mkdir -p $NXF_SINGULARITY_LIBRARYDIR
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- name: Conda setup
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if: contains(inputs.profile, 'conda')
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uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
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with:
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auto-update-conda: true
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conda-solver: libmamba
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channels: conda-forge
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channel-priority: strict
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conda-remove-defaults: true
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- name: Run nf-test
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shell: bash
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env:
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NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
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run: |
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nf-test test \
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--profile=+${{ inputs.profile }} \
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$(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
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--ci \
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--changed-since HEAD^ \
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--verbose \
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--tap=test.tap \
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--shard ${{ inputs.shard }}/${{ inputs.total_shards }}
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# Save the absolute path of the test.tap file to the output
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echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
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- name: Generate test summary
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if: always()
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shell: bash
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run: |
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# Add header if it doesn't exist (using a token file to track this)
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if [ ! -f ".summary_header" ]; then
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echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
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echo "" >> $GITHUB_STEP_SUMMARY
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echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY
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echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY
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touch .summary_header
99+
fi
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101+
if [ -f test.tap ]; then
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while IFS= read -r line; do
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if [[ $line =~ ^ok ]]; then
104+
test_name="${line#ok }"
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# Remove the test number from the beginning
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test_name="${test_name#* }"
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echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
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elif [[ $line =~ ^not\ ok ]]; then
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test_name="${line#not ok }"
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# Remove the test number from the beginning
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test_name="${test_name#* }"
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echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
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fi
114+
done < test.tap
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else
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echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
117+
fi
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119+
- name: Clean up
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if: always()
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shell: bash
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run: |
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sudo rm -rf /home/ubuntu/tests/

‎.github/workflows/awsfulltest.yml‎

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# It runs the -profile 'test_full' on AWS batch
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on:
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pull_request:
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branches:
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- main
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- master
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workflow_dispatch:
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pull_request_review:
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types: [submitted]
10+
release:
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types: [published]
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1513
jobs:
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run-platform:
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name: Run AWS full tests
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# run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
19-
if: github.repository == 'nf-core/proteinannotator' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
16+
# run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
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if: github.repository == 'nf-core/proteinannotator' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release'
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runs-on: ubuntu-latest
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steps:
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- name: Get PR reviews
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uses: octokit/request-action@v2.x
24-
if: github.event_name != 'workflow_dispatch'
25-
id: check_approvals
26-
continue-on-error: true
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with:
28-
route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
29-
env:
30-
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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32-
- name: Check for approvals
33-
if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
34-
run: |
35-
echo "No review approvals found. At least 2 approvals are required to run this action automatically."
36-
exit 1
37-
38-
- name: Check for enough approvals (>=2)
39-
id: test_variables
40-
if: github.event_name != 'workflow_dispatch'
20+
- name: Set revision variable
21+
id: revision
4122
run: |
42-
JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
43-
CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
44-
test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
23+
echo "revision={%- raw -%}${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
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- name: Launch workflow via Seqera Platform
4726
uses: seqeralabs/action-tower-launch@v2
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# TODO nf-core: You can customise AWS full pipeline tests as required
49-
# Add full size test data (but still relatively small datasets for few samples)
50-
# on the `test_full.config` test runs with only one set of parameters
5127
with:
52-
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
28+
workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
5329
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
54-
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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revision: ${{ github.sha }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/proteinannotator/work-${{ github.sha }}
30+
compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
31+
revision: ${{ steps.revision.outputs.revision }}
32+
workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/proteinannotator/work-${{ steps.revision.outputs.revision }}
5733
parameters: |
5834
{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/proteinannotator/results-${{ github.sha }}"
36+
"outdir": "s3://${{ vars.AWS_S3_BUCKET }}/proteinannotator/results-${{ steps.revision.outputs.revision }}"
6137
}
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profiles: test_full
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- uses: actions/upload-artifact@v4
40+
- uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
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with:
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name: Seqera Platform debug log file
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path: |
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seqera_platform_action_*.log
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seqera_platform_action_*.json
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tower_action_*.log
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tower_action_*.json

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