- Feb 14, 2020
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- add script `tests/test_rule_graph/test.sh` to generate a rule graph in `images/rule_graph.svg` - display rule graph created in `README.md` instead of specific workflow DAG - add test script to GitLab CI config - renamed test to create workflow DAG from `test_create_dag_chart` to `test_create_dag_image` (also output file is renamed from `images/workflow_dag.svg` to `images/dag_test_workflow.svg`
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- Feb 09, 2020
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Alex Kanitz authored
- replaces existing larger libraries and annotations in test cases `test_create_dag_chart` and `test_integration_workflow` - adds the following new test files: - `chr1-10000-20000.fa`: artificial chromosome of length 10'000 (based on human chromosome 1) - `chr1-10000-20000.gtf`: matching gene annotation file with two gene and three multi-exon transcripts entries - `chr1-10000-20000.transcripts.fa`: sequences of the transcripts listed in the gene annotation file - `synthetic.mate_?.fastq.gz`: 10 read pairs randomly sampled from the genic regions of the artificial chromosome - `synthetic.*.bed`: BED files with expected alignments for each read; names of overlapping genes are specified in a 7th column - updates file paths in the relevant sample tables - extends and updates checksum checking of result files in CI/CD pipeline
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- Feb 08, 2020
- Feb 04, 2020
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Alex Kanitz authored
- set up integration test for Snakefile in dedicated folder; current test case was left untouched for the time being, despite requiring large input files - set up DAG chart creation test in dedicated folder; script creates an SVG representation of the workflow DAG at `images/workflow_dag.svg` - both tests have been added to the GitLab CI/CD configuration; the latter test ensures that always the latest version of the - all tests are now located inside subdirectories of `tests/`; test scripts and configuration files for test runs etc. have been moved to the appropriate test directories - for the time being, required input files for each test are placed within the individual test directories; a layout for common test files should be introduced later and paths and bind paths in tests adapted - make script `scripts/labkey_api.py` executable
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