Use doi for all versions #77
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| name: fastq-dl | |
| on: | |
| push: | |
| branches: [ main, master, dev ] | |
| pull_request: | |
| branches: [ main, master, dev ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout rpetit3/fastq-dl | |
| uses: actions/checkout@v2 | |
| - uses: taiki-e/install-action@just | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: '3.10' | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| activate-environment: fastq-dl | |
| environment-file: environment.yml | |
| auto-update-conda: true | |
| - name: Install fastq-dl | |
| run: just install | |
| - name: Check formatting | |
| run: just check-fmt | |
| - name: Lint | |
| run: just lint | |
| - name: Test fastq-dl | |
| run: | | |
| fastq-dl --version | |
| fastq-dl --help | |
| - name: Test ENA Download | |
| run: | | |
| fastq-dl --accession SRX1390608 --outdir test-ena --verbose | |
| - name: Test ENA Metadata only | |
| run: | | |
| fastq-dl --accession SRX1390608 --outdir test-ena-metadata --verbose --only-download-metadata | |
| - name: Test SRA Download | |
| run: | | |
| fastq-dl --accession SRX1390608 --provider SRA --outdir test-sra --verbose | |
| - name: Test SRA Metadata only | |
| run: | | |
| fastq-dl --accession SRX1390608 --provider SRA --outdir test-sra-metadata --verbose --only-provider --only-download-metadata | |
| - name: Test Experiment with duplicate runs | |
| run: | | |
| fastq-dl --accession ERX012546 --provider sra --outdir test-duplicate --verbose | |
| - name: Test Small Run (SRA) | |
| run: | | |
| fastq-dl --accession SRX3606281 --provider SrA --outdir test-small-sra --verbose | |
| - name: Test Small Run (SRA) with --force | |
| run: | | |
| fastq-dl --accession SRX3606281 --provider SrA --outdir test-small-sra --verbose --force | |
| - name: Test Small Run (ENA) | |
| run: | | |
| fastq-dl --accession SRX3606281 --outdir test-small-ena --verbose | |
| - name: Test Small Run (ENA) with --force | |
| run: | | |
| fastq-dl --accession SRX3606281 --outdir test-small-ena --verbose --force | |
| - name: Test BioSample (ENA) | |
| run: | | |
| fastq-dl --accession SAMN06191622 --outdir test-biosample --verbose | |
| - name: Test Sample (SRA) | |
| run: | | |
| fastq-dl --accession SRS1904245 --provider SRA --outdir test-sample --verbose | |
| - name: Test --group-by-sample (ENA) | |
| run: | | |
| fastq-dl --accession SRS1904245 --outdir test-group-by-sample --verbose --group-by-sample | |
| - name: Test --group-by-experiment (SRA) | |
| run: | | |
| fastq-dl --accession ERX012546 --outdir test-group-by-experiment --verbose --group-by-sample |