Refactored metadata collection and fixes an issue with newly loaded datasets #12
Workflow file for this run
This file contains 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: Test Collect Metadata Script | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - series_id: GSE191067 | |
| subset_list: "" | |
| comment: "No ENA metadata" | |
| - series_id: GSE264508 | |
| subset_list: "" | |
| comment: ".fastq and .sra files in ENA metadata" | |
| - series_id: GSE274955 | |
| subset_list: "" | |
| comment: "Broken .sra files. Files in .bam format available" | |
| - series_id: GSE250130 | |
| subset_list: "" | |
| comment: "No Project or SubProjects in soft_family file" | |
| - series_id: E-MTAB-9221 | |
| subset_list: "" | |
| comment: "Regular ENA dataset" | |
| - series_id: GSE111360 | |
| subset_list: test_data/GSE111360/GSE111360.subset.list | |
| comment: "Subset list provided" | |
| - series_id: GSE117988 | |
| subset_list: "" | |
| comment: "Crap .fastq files, but .sra files are available in ENA metadata" | |
| - series_id: GSE160513 | |
| subset_list: "" | |
| comment: "Regular GEO dataset" | |
| - series_id: PRJNA511433 | |
| subset_list: "" | |
| comment: "Regular GEO dataset but using BioProject" | |
| name: "Test ${{ matrix.series_id }}: ${{ matrix.comment }}" | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Set up environment | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y wget perl curl jq | |
| - name: Run metadata collection tests | |
| run: | | |
| chmod +x ./scripts/* | |
| chmod +x ./tests/test_metadata.sh | |
| ./tests/test_metadata.sh ${{ matrix.series_id }} ${{ matrix.subset_list }} |