chore(deps): bump actions/checkout from 4.3.1 to 7.0.0 #9
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| name: Workflow integrations | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main] | |
| permissions: | |
| contents: read | |
| jobs: | |
| snakemake: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 | |
| - uses: dtolnay/rust-toolchain@4be7066ada62dd38de10e7b70166bc74ed198c30 # stable | |
| - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install pinned workflow tools | |
| run: | | |
| python -m pip install snakemake==9.8.1 | |
| sudo apt-get update | |
| sudo apt-get install -y samtools | |
| - name: Prepare indexed toy BAM and CLI | |
| run: | | |
| cargo build --locked --bin rosalind | |
| samtools view -b -F 4 examples/data/illumina_toy/alignments.bam | | |
| samtools sort -o examples/data/illumina_toy/sorted.bam | |
| samtools index examples/data/illumina_toy/sorted.bam | |
| echo "$PWD/target/debug" >> "$GITHUB_PATH" | |
| - name: Lint, dry-run, and execute local fan-in | |
| run: | | |
| snakemake --lint --snakefile integrations/snakemake/Snakefile \ | |
| --configfile integrations/snakemake/tests/config.yaml | |
| snakemake --dry-run --cores 1 --snakefile integrations/snakemake/Snakefile \ | |
| --configfile integrations/snakemake/tests/config.yaml | |
| snakemake --cores 1 --snakefile integrations/snakemake/Snakefile \ | |
| --configfile integrations/snakemake/tests/config.yaml | |
| test -s results/toy/merged.arrow | |
| test -s results/toy/merged.arrow.manifest.json | |
| test -s results/toy/verify.json | |
| nextflow: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 | |
| - uses: dtolnay/rust-toolchain@4be7066ada62dd38de10e7b70166bc74ed198c30 # stable | |
| - uses: actions/setup-java@c1e323688fd81a25caa38c78aa6df2d33d3e20d9 # v4 | |
| with: | |
| distribution: temurin | |
| java-version: '21' | |
| - uses: nf-core/setup-nextflow@98e3b21a1c45e26529208849ec20e5cfb7086040 # v2 | |
| with: | |
| version: '25.04.8' | |
| - name: Parse and execute the local shard graph | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y samtools | |
| cargo build --locked --bin rosalind | |
| mkdir -p "$RUNNER_TEMP/nextflow-inputs" | |
| samtools view -b -F 4 examples/data/illumina_toy/alignments.bam | | |
| samtools sort -o "$RUNNER_TEMP/nextflow-inputs/sample.bam" | |
| samtools index "$RUNNER_TEMP/nextflow-inputs/sample.bam" | |
| target/debug/rosalind reference build \ | |
| --fasta examples/data/illumina_toy/reference.fa \ | |
| --output "$RUNNER_TEMP/nextflow-inputs/reference.rref" | |
| nextflow -c integrations/nextflow/examples/local/nextflow.config \ | |
| config integrations/nextflow/examples/local/main.nf >/tmp/nextflow-config.txt | |
| PATH="$PWD/target/debug:$PATH" nextflow run integrations/nextflow/examples/local/main.nf \ | |
| -work-dir "$RUNNER_TEMP/nextflow-work" \ | |
| -with-trace "$RUNNER_TEMP/nextflow-trace.txt" \ | |
| -c integrations/nextflow/examples/local/nextflow.test.config \ | |
| --reference "$RUNNER_TEMP/nextflow-inputs/reference.rref" \ | |
| --bam "$RUNNER_TEMP/nextflow-inputs/sample.bam" \ | |
| --bai "$RUNNER_TEMP/nextflow-inputs/sample.bam.bai" \ | |
| --shard_count 2 \ | |
| --image local/rosalind@sha256:aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa | |
| awk -F '\t' 'NR > 1 && $5 != "COMPLETED" { exit 1 } END { if (NR != 8) exit 1 }' \ | |
| "$RUNNER_TEMP/nextflow-trace.txt" |