Use fromSamplesheet #738
Workflow file for this run
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| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| name: nf-core CI | |
| on: | |
| push: | |
| branches: | |
| - "dev" | |
| pull_request: | |
| branches: | |
| - "dev" | |
| - "master" | |
| release: | |
| types: | |
| - "published" | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFTEST_VER: "0.7.3" | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| aligner: | |
| - "bismark" | |
| - "bismark_hisat" | |
| - "bwameth" | |
| profile: | |
| - "docker" | |
| steps: | |
| # Skip if it's a pull_request to dev and NXF_VER is '22.10.1' | |
| - name: Skip condition | |
| id: condition | |
| run: | | |
| if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then | |
| echo "skip=true" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Check out pipeline code | |
| if: steps.condition.outputs.skip != 'true' | |
| uses: actions/checkout@v3 | |
| - name: Hash Github Workspace | |
| if: steps.condition.outputs.skip != 'true' | |
| id: hash_workspace | |
| run: | | |
| echo "digest=$(echo methylseq2_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT | |
| - name: Cache test data | |
| if: steps.condition.outputs.skip != 'true' | |
| id: cache-testdata | |
| uses: actions/cache@v3 | |
| with: | |
| path: test-datasets/ | |
| key: ${{ steps.hash_workspace.outputs.digest }} | |
| - name: Check out test data | |
| if: steps.cache-testdata.outputs.cache-hit != 'true' && steps.condition.outputs.skip != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: nf-core/test-datasets | |
| ref: methylseq | |
| path: test-datasets/ | |
| - name: Replace remote paths in samplesheets | |
| if: steps.condition.outputs.skip != 'true' | |
| run: | | |
| for f in ./test-datasets/samplesheet/*csv; do | |
| sed -i 's=https://github.com/nf-core/test-datasets/raw/methylseq/=./test-datasets/=g' $f | |
| sed -i 's=https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/=./test-datasets/=g' $f | |
| echo "========== $f ============" | |
| cat $f | |
| echo "========================================" | |
| done; | |
| - name: Install Nextflow | |
| if: steps.condition.outputs.skip != 'true' | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Install nf-test | |
| if: steps.condition.outputs.skip != 'true' | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: Run nf-test | |
| if: steps.condition.outputs.skip != 'true' | |
| run: | | |
| nf-test test tests/pipeline/${{ matrix.aligner }}/ --profile "test,${{ matrix.profile }}" --tap=test.tap | |
| # If the test fails, output the software_versions.yml using the 'batcat' utility | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml |