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Merge pull request #492 from nf-core/dev
Dev -> Master 3.0.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| name: "Get number of shards" | ||
| description: "Get the number of nf-test shards for the current CI job" | ||
| inputs: | ||
| tags: | ||
| description: "Tags to pass as argument for nf-test --tag parameter" | ||
| required: true | ||
| max_shards: | ||
| description: "Maximum number of shards allowed" | ||
| required: true | ||
| outputs: | ||
| shard: | ||
| description: "Array of shard numbers" | ||
| value: ${{ steps.shards.outputs.shard }} | ||
| total_shards: | ||
| description: "Total number of shards" | ||
| value: ${{ steps.shards.outputs.total_shards }} | ||
|
|
||
| runs: | ||
| using: "composite" | ||
| steps: | ||
| - name: Install nf-test | ||
| uses: nf-core/setup-nf-test@v1 | ||
| with: | ||
| version: ${{ env.NFT_VER }} | ||
| install-pdiff: true | ||
|
|
||
| - name: Get number of shards | ||
| id: shards | ||
| shell: bash | ||
| run: | | ||
| # Run nf-test to get the number of related tests | ||
| nftest_output=$(nf-test test --dry-run --changed-since HEAD^ --filter pipeline --tag ${{ inputs.tags }}) | ||
| echo "nf-test dry-run output: $nftest_output" | ||
| # Default values for shard and total_shards | ||
| shard="[]" | ||
| total_shards=0 | ||
| # Check if there are related tests | ||
| if echo "$nftest_output" | grep -q 'Nothing to do'; then | ||
| echo "No related tests found." | ||
| else | ||
| # Extract the number of related tests | ||
| number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p') | ||
| if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then | ||
| shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} )) | ||
| shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .) | ||
| total_shards="$shards_to_run" | ||
| else | ||
| echo "Unexpected output format. Falling back to default values." | ||
| fi | ||
| fi | ||
| # Write to GitHub Actions outputs | ||
| echo "shard=$shard" >> $GITHUB_OUTPUT | ||
| echo "total_shards=$total_shards" >> $GITHUB_OUTPUT | ||
| # Debugging output | ||
| echo "Final shard array: $shard" | ||
| echo "Total number of shards: $total_shards" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| name: "nf-test Action" | ||
| description: "Runs nf-test with common setup steps" | ||
| inputs: | ||
| profile: | ||
| description: "Profile to use" | ||
| required: true | ||
| shard: | ||
| description: "Shard number for this CI job" | ||
| required: true | ||
| total_shards: | ||
| description: "Total number of test shards(NOT the total number of matrix jobs)" | ||
| required: true | ||
| filters: | ||
| description: "Filter test cases by specified types (e.g., module, pipeline, workflow or function)" | ||
| required: true | ||
| tags: | ||
| description: "Tags to pass as argument for nf-test --tag parameter" | ||
| required: true | ||
|
|
||
| runs: | ||
| using: "composite" | ||
| steps: | ||
| - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4 | ||
| with: | ||
| distribution: "temurin" | ||
| java-version: "17" | ||
|
|
||
| - name: Setup Nextflow | ||
| uses: nf-core/setup-nextflow@v2 | ||
| with: | ||
| version: "${{ env.NXF_VER }}" | ||
|
|
||
| - name: Set up Python | ||
| uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | ||
| with: | ||
| python-version: "3.11" | ||
|
|
||
| - name: Install nf-test | ||
| uses: nf-core/setup-nf-test@v1 | ||
| with: | ||
| version: "${{ env.NFT_VER }}" | ||
| install-pdiff: true | ||
|
|
||
| - name: Setup apptainer | ||
| if: contains(inputs.profile, 'singularity') | ||
| uses: eWaterCycle/setup-apptainer@main | ||
|
|
||
| - name: Set up Singularity | ||
| if: contains(inputs.profile, 'singularity') | ||
| shell: bash | ||
| run: | | ||
| mkdir -p $NXF_SINGULARITY_CACHEDIR | ||
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | ||
| - name: Conda setup | ||
| if: ${{inputs.profile == 'conda'}} | ||
| uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3 | ||
| with: | ||
| auto-update-conda: true | ||
| conda-solver: libmamba | ||
| conda-remove-defaults: true | ||
|
|
||
| - name: Run nf-test | ||
| shell: bash | ||
| run: | | ||
| NFT_WORKDIR=~ \ | ||
| nf-test test \ | ||
| --ci \ | ||
| --shard ${{ inputs.shard }}/${{ inputs.total_shards }} \ | ||
| --changed-since HEAD^ \ | ||
| --profile=${{ inputs.profile }} \ | ||
| --filter ${{ inputs.filters }} \ | ||
| --tap=test.tap \ | ||
| --verbose \ | ||
| --tag ${{ inputs.tags }} | ||
| # TODO If no test.tap, then make one to spoof? | ||
| - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 | ||
| if: ${{ inputs.path != '' }} | ||
| with: | ||
| path: >- | ||
| test.tap | ||
| - name: Clean up | ||
| if: always() | ||
| shell: bash | ||
| run: | | ||
| sudo rm -rf /home/ubuntu/tests/* |
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