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  1. Mar 12, 2020
    • Dominik Burri's avatar
      replaced synthetic test by new one. · 46e6e00b
      Dominik Burri authored
      moved input_files into top-layer test directory for consistency.
      
      corrected removal of test files
      46e6e00b
    • Dominik Burri's avatar
      added rule for · 37fb0fd0
      Dominik Burri authored
      - renaming bedgraph
      - creating ALFA qc plots
      
      removed conda dependence, moved import statement.
      
      included ALFA in finish rule, corrected annotation.gtf and config.yaml, created new .svg
      37fb0fd0
  2. Feb 20, 2020
    • Alex Kanitz's avatar
      create log directories in Snakefile\ · 5e1ec85e
      Alex Kanitz authored
      - log and, if workflow is executed on cluster, cluster log directories are explicitly created in `Snakefile`
      - location of main log directory can be configured in `config.yaml` (field `log_dir`, previously: `local_log`; requires change in script `labkey_to_snakemake.py` as well as subworkflows as field name is hard-coded there)
      - location of cluster log directory can be configured in `cluster.json` (in field `__default__` -> `out`)
      - `config.yaml` and `cluster.json` in `tests/input_files` are set such that a directory `logs/` is created in the directory where Snakemake is run (i.e., the directory of each test); cluster logs are stored in a subdirectory `logs/cluster`
      - removes instructions to explicitly create log directories from docs and all test scripts
      - cleans up main `Snakefile` (apart from Snakemake-specific syntax, now passes `flake8` linter test)
      5e1ec85e
  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
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