- Mar 12, 2020
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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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- Mar 06, 2020
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BIOPZ-Gypas Foivos authored
Merged paired end and single end rules for star_rpm and index_genomic_alignment_samtools. Fixed wiring of calculate tin score: bam should be input and not params.
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- Feb 21, 2020
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Alex Kanitz authored
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- Remove files with non-deterministic output from `tests/test_integration_workflow/expected_output.files` - Update MD5 sums in `tests/test_integration_workflow/expected_output.md5` - Update new workflow DAG and rule graph images
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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 14, 2020
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Alex Kanitz authored
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- Feb 08, 2020
- Feb 07, 2020
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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
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- Jan 24, 2020
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BIOPZ-Gypas Foivos authored
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- replace corrupt input files - add script that runs locally named `run_test.sh` in the snakemake directory - add script to CI/CD pipeline - fix typo in `paired_end.snakefile` - update samples.tsv with fake adapter `XXXXXXX` when we do not want to trim them
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- Dec 20, 2019
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BIOPZ-Gypas Foivos authored
Rename snakemake/paired_end.snakemake to snakemake/paired_end.snakefile. Fix wiring of rules. Add fake tests.
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BIOPZ-Gypas Foivos authored
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BIOPZ-Iborra de Toledo Paula authored
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