Refactor the XAVIER GUI #141
Workflow file for this run
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| name: tests | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| - unified | |
| pull_request: | |
| branches-ignore: [] | |
| jobs: | |
| dryrun-lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: docker://snakemake/snakemake:v7.32.4 | |
| - name: check CLI basics | |
| run: | | |
| ./bin/xavier --help | |
| ./bin/xavier --version | |
| - name: Tumor-normal FastQ Dry Run | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ | |
| /opt2/bin/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \ | |
| /opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \ | |
| /opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.R2.fastq.gz \ | |
| --output /opt2/output_tn_fqs --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ | |
| /opt2/bin/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \ | |
| /opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \ | |
| /opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.R2.fastq.gz \ | |
| --output /opt2/output_tn_fqs --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun | |
| - name: Tumor-only FastQ Dry Run | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ | |
| /opt2/bin/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \ | |
| /opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \ | |
| /opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.R2.fastq.gz \ | |
| --output /opt2/output_tonly_fqs --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --genome hg38 --mode local --ffpe --runmode init | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ | |
| /opt2/bin/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \ | |
| /opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \ | |
| /opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.R2.fastq.gz \ | |
| --output /opt2/output_tonly_fqs --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --genome hg38 --mode local --ffpe --runmode dryrun | |
| - name: Tumor-normal BAM Dry Run | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ | |
| /opt2/bin/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.recal.bam \ | |
| /opt2/.tests/Sample11_ACI_158_S38.recal.bam \ | |
| /opt2/.tests/Sample4_CRL1622_S31.recal.bam \ | |
| --output /opt2/output_tn_bams --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ | |
| /opt2/bin/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.recal.bam \ | |
| /opt2/.tests/Sample11_ACI_158_S38.recal.bam \ | |
| /opt2/.tests/Sample4_CRL1622_S31.recal.bam \ | |
| --output /opt2/output_tn_bams --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun | |
| - name: Tumor-only BAM Dry Run | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ | |
| /opt2/bin/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.recal.bam \ | |
| /opt2/.tests/Sample11_ACI_158_S38.recal.bam \ | |
| /opt2/.tests/Sample4_CRL1622_S31.recal.bam \ | |
| --output /opt2/output_tonly_bams --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --genome hg38 --mode local --ffpe --runmode init | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ | |
| /opt2/bin/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.recal.bam \ | |
| /opt2/.tests/Sample11_ACI_158_S38.recal.bam \ | |
| /opt2/.tests/Sample4_CRL1622_S31.recal.bam \ | |
| --output /opt2/output_tonly_bams --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --genome hg38 --mode local --ffpe --runmode dryrun | |
| - name: Lint | |
| continue-on-error: true | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output_tn_fqs || \ | |
| echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.' | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.11"] | |
| snakemake-version: ["7.32.4"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: test | |
| cache-environment: true | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| snakemake=${{ matrix.snakemake-version }} | |
| setuptools | |
| pip | |
| pytest | |
| - name: check CLI basics | |
| run: | | |
| ./bin/xavier --help | |
| ./bin/xavier --version | |
| shell: micromamba-shell {0} | |
| - name: pip install python package | |
| run: | | |
| pip install .[dev,test] | |
| shell: micromamba-shell {0} | |
| - name: Test | |
| run: | | |
| python -m pytest | |
| env: | |
| TMPDIR: ${{ runner.temp }} | |
| shell: micromamba-shell {0} | |
| build-status: # https://github.com/orgs/community/discussions/4324#discussioncomment-3477871 | |
| runs-on: ubuntu-latest | |
| needs: [dryrun-lint, test] | |
| if: always() | |
| steps: | |
| - name: Successful build | |
| if: ${{ !(contains(needs.*.result, 'failure')) }} | |
| run: exit 0 | |
| - name: Failing build | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 |