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  1. Oct 16, 2020
  2. Jun 15, 2020
  3. Apr 27, 2020
    • Alex Kanitz's avatar
      Refactor LabKey to Snakemake script · 556f1e12
      Alex Kanitz authored
      - clean up command line interface
        - improve descriptions
        - add consistent structure
        - remove or merge superfluous CLI arguments
        - set defaults
        - update test calls
        - update docs
        - when importing data from LabKey, table is saved to 'samples.tsv.labkey' in same directory as Snakemake sample table
      - allow user to specify environment variables and relative paths in input table and on CLI
        - relative paths in the input table are interpreted with respect to the directory containing the input table
        - relative paths will are interpreted with respect to the current working directory; this is to achieve portability with respect to tests but is discouraged in production because its behavior is not very predictable from the user's perspective; consequently a warning is thrown
      - set STAR index size to read length - 1
      - remove `gtf_filtered` and `tr_fasta_filtered` and update Snakefiles and test sample tables accordingly
      - rename some MultiQC report-related parameters and update Snakefiles and test config files accordingly
      - add logging
      - add docstrings to module and all functions
      - add typing definitions to all functions
      - restructure and comment code to improve readability
      - linters `flake8` and `mypy` pass
      556f1e12
    • BIOPZ-Katsantoni Maria's avatar
      Major refactoring · 6cf28511
      BIOPZ-Katsantoni Maria authored and Alex Kanitz's avatar Alex Kanitz committed
      * Sequencing mode-related changes:
        * allowed sequencing modes in Snakemake input table changed from `paired_end` and `single_end` to `pe` and `se`, respectively
        * remove sequencing mode from output paths for each rule
        * corresponding wild cards removed entirely from all rules that do not depend on sequencing mode (currently all rules that are defined in the main `Snakefile` in the project root directory)
        * where absolutely necessary, sequencing mode is added as part of output file or directory instead
        * remove dependency of sequencing mode for rule for `FastQC`; now runs separately for each strand
      * Changes related to MultiQC and output file/directory structure
        * moving and renaming outputs for MultiQC is no longer required
        * code to create MultiQC custom config externalized into script `scripts/rhea_multiqc_config.py`
        * add MultiQC output files with deterministic output to md5 sum checks performed during execution of `tests/test_integration_workflow/test.{local,slurm}.sh`
        * output filenames for each rule now follow this general structure: `samples/{sample_name}/{rule}/{output_file}`
        * change log directory structure matches results directory structure
      * Miscellaneous changes
        * consistent, PEP8-compliant formatting in most parts, including Snakemake files, where allowed
        * remove rule `extract_decoys_salmon`; equivalent file `chrName.txt` produced by `star_index` is used instead
        * add rule `start` which copies sample data to the results directory and enforces uniform naming
        * refactoring of ALFA rules and modification of the CI/CD test to ensure compatibility
      6cf28511
    • CJHerrmann's avatar
      Add rules for bigWig creation · 907082c3
      CJHerrmann authored and Alex Kanitz's avatar Alex Kanitz committed
      907082c3
  4. Mar 25, 2020
  5. Mar 21, 2020
  6. Mar 20, 2020
  7. Mar 19, 2020
  8. Mar 12, 2020
  9. Mar 06, 2020
  10. Feb 24, 2020
  11. Feb 21, 2020
  12. 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
  13. 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
  14. 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
  15. 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
  16. Feb 08, 2020
  17. 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
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