- Mar 12, 2020
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Dominik Burri authored
moved input_files into top-layer test directory for consistency. corrected removal of test files
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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
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- Feb 20, 2020
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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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- Feb 15, 2020
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- 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
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