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    5e1ec85e
    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
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    create log directories in Snakefile\
    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)
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