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  1. Mar 06, 2020
  2. Feb 21, 2020
  3. 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
  4. 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
  5. Feb 14, 2020
  6. Feb 08, 2020
  7. Feb 07, 2020
    • Alex Kanitz's avatar
      fix various small issues · 17818f4a
      Alex Kanitz authored
      - remove log files and add '.snakemake' directories to '.gitignore'
      - update wrong link in 'README.md'
      - delete superfluous script documentation 'scripts/labkey_api.md'
      - add Snakemake-specific file extension '.smk' to subworkflows
      - remove non-deterministic workflow output from md5 sums
      17818f4a
  8. Jan 24, 2020
  9. Dec 20, 2019
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