Skip to content
Snippets Groups Projects
  1. Feb 21, 2020
  2. Feb 17, 2020
    • BIOPZ-Bak Maciej's avatar
      add TIN score calculation · c538fe8b
      BIOPZ-Bak Maciej authored and Alex Kanitz's avatar Alex Kanitz committed
      - add rule for input preparation (GTF to BED12)
      - add rule for TIN score calculation
      - update rule graph and DAG image
      - update Slurm cluster config
      c538fe8b
  3. Feb 15, 2020
    • BIOPZ-Katsantoni Maria's avatar
      get Snakemake input from LabKey API · eea0206f
      BIOPZ-Katsantoni Maria authored and Alex Kanitz's avatar Alex Kanitz committed
      - add script that prepares Snakemake input files 'samples.tsv' and 'config.yaml' from LabKey table
      - script either connects to API directly (with '--remote' and related options) or processes a tab-separated LabKey dump file
      - add tests for both use cases
      - common input files for tests now in 'tests/input_files'
      - update all other tests to account for new file locations
      - update documentation
      eea0206f
  4. Feb 14, 2020
    • BIOPZ-Katsantoni Maria's avatar
      LabKey-like input to Snakmake input · 979e6cdd
      BIOPZ-Katsantoni Maria authored and Alex Kanitz's avatar Alex Kanitz committed
      - separate organism genome architecture (different input folder)
      - change MD5 checksums to match the new output
      979e6cdd
    • CJHerrmann's avatar
      display rule graph instead of DAG · ff08b9c3
      CJHerrmann authored and Alex Kanitz's avatar Alex Kanitz committed
      - 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`
      ff08b9c3
  5. Feb 09, 2020
    • Alex Kanitz's avatar
      replace test files with small synthetic ones · 48e012a0
      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
      48e012a0
  6. Feb 08, 2020
  7. Feb 04, 2020
    • Alex Kanitz's avatar
      clean up tests · 6a231363
      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
      6a231363
Loading