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Merge pull request #42 from nf-core/olgabot/add-nf-test-config-v2
Add nf-test configuration and gitignore
2 parents e4c57d3 + a3e8064 commit 90f83a9

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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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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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--dry-run \
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--profile +docker \
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--filter function,workflow,pipeline \
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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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runs:
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using: "composite"
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steps:
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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: "${{ env.NXF_VERSION }}"
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- name: Set up Python
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uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
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with:
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python-version: "3.11"
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- name: Install nf-test
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uses: nf-core/setup-nf-test@v1
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with:
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version: "${{ env.NFT_VER }}"
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- name: 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: ${{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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conda-remove-defaults: true
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- name: Install pdiff
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shell: bash
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run: |
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python -m pip install pdiff
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- name: Clean up Disk space
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uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
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# TODO Skip failing conda tests and document their failures
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# https://github.com/nf-core/modules/issues/7017
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- name: Run nf-test
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shell: bash
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env:
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NFT_DIFF: ${{ env.NFT_DIFF }}
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NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
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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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--tap=test.tap \
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--verbose \
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--ci \
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--changed-since HEAD^ \
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--shard ${{ inputs.shard }}/${{ inputs.total_shards }} \
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--filter function,workflow,pipeline
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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
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fi
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if [ -f test.tap ]; then
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while IFS= read -r line; do
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if [[ $line =~ ^ok ]]; then
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test_name="${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
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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
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fi
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- 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]
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release:
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types: [published]
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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/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'
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# run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
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if: github.repository == 'nf-core/rnavar' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
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runs-on: ubuntu-latest
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steps:
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- name: Set revision variable
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id: revision
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- name: Get PR reviews
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uses: octokit/request-action@v2.x
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if: github.event_name != 'workflow_dispatch'
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id: check_approvals
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continue-on-error: true
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with:
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route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Check for approvals
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if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
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run: |
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echo "No review approvals found. At least 2 approvals are required to run this action automatically."
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exit 1
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- name: Check for enough approvals (>=2)
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id: test_variables
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if: github.event_name != 'workflow_dispatch'
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run: |
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echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
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JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
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CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
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test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
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- name: Launch workflow via Seqera Platform
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uses: seqeralabs/action-tower-launch@v2
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# TODO nf-core: You can customise AWS full pipeline tests as required
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# Add full size test data (but still relatively small datasets for few samples)
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# on the `test_full.config` test runs with only one set of parameters
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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revision: ${{ steps.revision.outputs.revision }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/proteinannotator/work-${{ steps.revision.outputs.revision }}
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revision: ${{ github.sha }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnavar/work-${{ github.sha }}
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/proteinannotator/results-${{ steps.revision.outputs.revision }}"
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnavar/results-${{ github.sha }}"
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}
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profiles: test_full
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‎.github/workflows/ci.yml‎

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