Fix post-overhaul integration gates #10
Workflow file for this run
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Workflow integrations | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main] | |
| permissions: | |
| contents: read | |
| jobs: | |
| snakemake: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4 | |
| - 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@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4 | |
| - 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" |